Extracts amino acid sequence that corresponds to structure in PDB
Parses a FSOLVText report into a FeatureAASequence (the feature is DPS DG)
Given a pdbCode returns a prot-prot interface
Parses a PMUTText report into a FeatureAASequence. Value is patogenicity prediction
Produces full amino acid sequence that corresponds to a PDB entry
Retrieves structure from PDB (PDB format) from a PDB Id Allows to specify a single chain using the format XXXX_X.
Parses secondary structure from a PHD report following the Profile network prediction HeiDelberg
Perform 2 iterations of protein PSI Blast against non-redundant database with standard settings
Retrieves headers from a PDB entry in PDB format
Performs secondary structure and accessibility predictions using PHD
Given a PDB Ligand code, returns information about the ligand
Evaluates fractional solvation based on LRT method
Returns a 2D graphic from a FeatureAASequence (png image)
Parses accessibility from a PHD report, where: b = 0-9%, i = 9-36%, e = 36-100%
Given a PDB code and a PDB Ligand code, returns the PDB-text of the ligand into this PDB structure
Predicts sequence positions (Hot Spots) that would produce pathological behaviour when mutated. Trained with human pathological mutations
Given a PDB code, returns all the components of the protein
Predicts secondary structure and accessibility using PHD program
Given a PDB code, returns all the protein fragments that interact with a ligand
Parses a PMUTText report into a PropertySequence (where N means NEUTRAL and H means HOT-SPOT)
Produces a multiple alignment in FASTA format from Blast Hits.
Parses a FSOLVText report into a PropertySequence (where N means NORMAL and O means OUTSIDE)
Given a PDB code, returns all the ligands Id associated to it
Given a Ligand code, returns all the PDB codes that contain this ligand
consumes EMBL id and returns a FASTA object
Retrieve SNPs from 19 strains of Arabidopsis thaliana. SNPs were resequenced using whole genome oligonucleotide arrays from Perlegen science and were predicted using SVMs at the Weigel-Lab (MPI Tuebingen, Germany).
Mapping of nucleotide sequences to any fasta annotation like releases for genomes , genes, miRNAs and repeatable elements for any organism. Allows Mismatches.
Retrieve SNPs in coding regions from 19 strains of Arabidopsis thaliana. SNPs were resequenced using whole genome oligonucleotide arrays from Perlegen science and were predicted using SVMs at the Weigel-Lab (MPI Tuebingen, Germany).
Retrieve deletions from 19 strains of Arabidopsis resequenced with whole genome oligonucleotide array from Perlegen Sciences.
A MOBY service that accepts a taxon name (the full name of a species) and return the list of geographical coordinates where such species was collected in database: <<<databaseName>>>. An example of input name is: Vicia faba (which is is a species of bean (Fabaceae) native to north Africa and southwest Asia, and extensively cultivated elsewhere.) The service has also a paging mechanism: a client can ask either all results in one call, or ask to get separate results (see secondary inputs for paging).
This service takes a GO Id (ex : GO:0050661), or a list of gene id associated. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana) according to the namespace given (OryGenesDB_Oryza or OryGenesDB_Arabidopsis).
This service takes a gene identifier (ex : Os03g51030 or Os03g51030.1), or a list of them, and returns associated flanking sequence tags (fst) and fst informations about the gene. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana) according to the namespace given (OryGenesDB_Oryza or OryGenesDB_Arabidopsis).
Get genes in OryGenesDB by using keywords (strings).
Blast on OrygenesDB (orygenesdb.cirad.fr)
Genes in TIGR Rice Pseudomolecules : Genomic sequences
Genes in TIGR Rice Pseudomolecules : CDS sequences
Genes in TIGR Rice Pseudomolecules : Protein sequences
cDNA Full Length (KOME) : Nucleic sequences
Oryza BAC Library Project : Nucleic sequences
Get genes in OryGenesDB by using GO term or GO ID.
This service takes a gene identifier (ex : Os03g51030 or Os03g51030.1), or a list of them, and returns associated informations about the gene. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana) according to the namespace given (OryGenesDB_Oryza or OryGenesDB_Arabidopsis).
This service takes a FST identifier (ex : CL524683), or a list of them, and returns a list of associated gene identifiers. The service works only with the rice specie (Oryza sativa namespace).
This service takes a gene identifier (ex : Os03g51030 or Os03g51030.1), or a list of them, and returns associated flanking sequence tags (fst) in order to join the web service 'getGermplasmByFST' (oryzataglines.cirad.fr). The service works with Oryza sativa species only.
Take a location (ex : 1:1..20000) and returns a list of gene identifiers. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana) according to the namespace given (OryGenesDB_Oryza or OryGenesDB_Arabidopsis).
This service takes a gene identifier (ex : Os01g18620 or Os01g18620.1), or a list of them, and returns EST details about this gene. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana) according to the namespace given (OryGenesDB_Oryza or OryGenesDB_Arabidopsis).
This service takes a gene identifier (ex : Os03g51030 or Os03g51030.1), or a list of them, and returns associated Swissprot details. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana) according to the namespace given (OryGenesDB_Oryza or OryGenesDB_Arabidopsis).
Returns an EvocDIGDescription given an EvocID
Returns the name of an Evoc Concept given its EvocID
Returns a collection of CDNALibraries given an EvocDIGDescription
Returns a collection of EvocIDs given a CDNA Library ID
Retrieves an aminoacid sequence from an aminoacid database.
Compares a protein sequence to a sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
RENCI's impl for the RegisterService interface
initial testing of a base service implementation for RENCI
Synthetic Lethal Interactions from Tong et al. (2001) stored in the GRID.
Takes any text (abstract, full text article, etc.) and extracts names and abbreviations of genes and proteins, with a score (0-1, with 1 being highest).
Runs the Smith Waterman pairwise alignment software for a query against all publically available DNA or AA
Runs the BLAST pairwise alignment software for a query against all publically available DNA or AA sequence
Transforms FASTA text into DNASequence, primarily for service inter-operability
searches the query sequence against the Pfam protein domain database
takes a collection of a unique input object related to accessions selection criteria and returns a collection of output objects representing accessions in the MGIS database.
returns different kinds of distance matrices built from a complete disjunctive matrix using R
returns different kinds of distance matrices built from a complete disjunctive matrix using R. All these distances are of type d = p1 - s with s a similarity coefficient. (parameter: for instance 1 = Jaccard. for further information see http://cran.r-project.org/ package ade4 method dist.binary)
takes a list of criteria and returns a collection of accessions in the MGIS database.
Code of the collection maintaining the germplasm: BPI (DAVAO), Philippines (DAV) IIHR, India (IIH) ITC, Belgium (ITC) NARO-KARI (KAWANDA), Uganda (KAW) KARI, Kenya (KIS) NARI-LALOKI, Papua New Guinea (LAL) FHIA, Honduras (LIM) CIRAD/FLHOR (GLP), Guadeloupe (NEU) CARBAP (NYOMBE), Cameroon (NYO) IITA (ONNE), Nigeria (ONN) PHU HO FCRC, Viet Nam (PHU) RIF-SOLOK, Indonesia (RIF) SCAU, China (SCU) QDPI-SOUTH JOHNSTONE, Australia (SJR) KAU, India (THR) NRCB, India (TRY)
Country code of the country source of this germplasm: BRA=Brazil CHN=China CMR=Cameroon CRI=Costa Rica CUB=Cuba DOM=Dominican Rep. HND=Honduras IDN=Indonesia IND=India JAM=Jamaica KEN=Kenya MTQ=Martinique NGA=Nigeria PAN=Panama PHL=Philippines PNG=Papua New Guinea PRI=Puerto Rico SLB=Solomon Islands SGP=Singapore TTO=Trinidad and Tobago TZA=Tanzania UGA=Uganda USA=United States VNM=Viet Nam
returns a neighbour joining tree built from a distance matrix using R and creates a file in the NEXUS format
Melting: enthalpie, entropy and melting temperature (N. Le Novere)
This service takes a gene identifier (ex : Os02g32430.1), or a list of them, and returns an image about the gene. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana) according to the namespace given (GreenPhylDB_Oryza or GreenPhylDB_Arabidopsis).
GOST is a powerful tool developed to predict phylogenomic relationships between any plant gene and O. sativa / A. thaliana gene(s). This tool is able to rapidly integrate a new sequence into a model phylogeny developed on O.sativa and A.thaliana to infer orthologs relationships. It takes as input a protein sequence and a greenphyl family id (obtained by blast on greenphyldb) which was analysed. It returns ortholgs predictions with scores and a NHX tree.
Send a crop name and return a species name compliant with the GOST species tree
Find similarity (blastp) with greenphyl protein families
This service takes a gene identifier (ex : Os03g51030), or a list of them, and returns an image about the gene. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana) according to the namespace given (GreenPhylDB_Oryza or GreenPhylDB_Arabidopsis).
This service takes a gene identifier (ex : At1g01010.1), or a list of them, and returns an image about the gene. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana)
Takes an interpro domain identifier (ie : IPR000005 ) and returns a collection of Gene id. The service works with the 2 species (Oryza sativa or Arabidopsis thaliana) according to the namespace given (GreenPhylDB_Oryza or GreenPhylDB_Arabidopsis).
test for SSWAP FASTA sequence lookup resource check "Fill new Service when selected in browser panel
Search TIGR Arabidopsis Reporter Image Database by Locus Name (or unassigned, such as At.chr5.3.34) Based on Arabidopsis project at: http://www.tigr.org/tdb/e2k1/ath1/qpcr/expression.php
Submit a Blast Job and retrieve a Job ID. Use Job ID with the RetrieveJob service from the same service provider to fetch the results.
Retrieve service options including a list of available databases. Input is an empty BioMOBY object. Output is an empty response with options documented in the ServiceNotes section of the header.
Retrieve service options including a list of BLASTable databases. Input is an empty BioMOBY object. Output is an empty response with options documented in the ServiceNotes section of the header.
BioMOBY web service wrapper for the command line query tool 'BLAT'.
Retrieve the result of the MobyBlast_submit service. Input is the output of the MobyBlast_submit service.
BioMOBY web service interface to the command line query tool 'getz' from SRS.
Returns your BioMOBY compliant input. Can be used to check client-server communication. Handles Simple, Collection and Secondary inputs.
Submit the result of the MobyBlast_submit service and obtain status info for the job.
Takes a Schematikon structure segment or structure motif ID and returns its attributes (PDB id, chain ID, chain position (starting residue), insert code, length)
Takes a PDB id and returns all associated Schematikon Motif IDs
Takes a Schematikon structure segment or structure motif ID and returns amino acid sequence
Takes a Schematikon structure motif ID and returns support and unique support for that motif
Takes a Schematikon structure motif ID and returns a list of neighbouring segments within the Voronoi domain of the motif
Takes a Schematikon structure segment or structure motif ID and returns DSSP, STRIDE, and PROMOTIF annotations
Takes a PDB id and returns all associated Schematikon Segment IDs
Takes a Schematikon structure motif ID and returns a list of neighbouring segments within 0.2 angstrom RMSD
Test service: matches NCBI_Acc to RGD gene RGD ID and Symbol, if available
A prediction service for identifying putative N-terminal targeting sequences (with Plant ID)
returns Genefarm GENE_ID(s) corresponding to an AGI_LocusCode
returns the biochemical function of a specific gene
returns Genefarm GENE_ID(s) belonging to a Family
Access to Phytoprot's clusters, by accession number
Access to Phytoprot's clusters by Cluster ID
returns the family name related to a genefarm Family identifier
returns the GeneFarm gene_ID(s) belonging to same gene family as the given gene ID
returns GeneFarm gene identifiers whose function matchs a keyword
returns the gene names corresponding to a gene ID
returns the organism name related to a gene id
returns the Genefarm Family identifier of a gene
Access to Phytoprot's clusters by keyword
returns family identifiers corresponding to a function keywordi
returns the Genefarm annotators names for a given gene
Access to Phytoprot's clusters by amino acid sequence
returns Genefarm GENE_ID(s) corresponding to a gene name
Retrieve a family's Pyramid file from Phytoprot database.
A prediction service for identifying putative N-terminal targeting sequences (without Plant ID)
returns the cultivar related to a gene id
Retrieval a family's XDOM from Phytoprot database.
This service returns germplasm's Intelectual Property using germplasm Id.
Retrieves the ontology term details given the Ontology Term LSID. Sample input: urn:lsid:generationcp.org:OntologyTerm:GCP_200.0000001
Retrieves a list of associated studies given a GCP entity. Sample input germplasm id: 50533
Retrieves full details about specified rice germplasm. Sample input germplasm id: 50533
return a collection of GCP_SimpleIdentifier objects for WhiteBoard
This service returns germplasm's Biological Status using germplasm Id.
Retrieves ontology term ids given the ontology term name. Sample input: junction
This service returns germplasm's acquisition date using germplasm Id.
returns a list of mutant germplasm identifiers phenotyped by trait
Retrieves the list of all germplasm identifiers (belonging to the Management Neighbourhood) of the given Accession. Sample input accession id 313137
Retrieve list of germplasm identifiers whose names match the given search string. For example, you may input the search string of a germplasm name "IR 64"
Retrieves the accession that a given germplasm belongs to. Sample input id 1636780.
Retrieves all clone names for given chromosome number
executes blast against MAtDB Arabidopsis protein coding genes with a cutoff E-value of E=1e-13
parses Element Names out of any text-xml or text-formatted (output sorted by alphabet)
returns URL(s) of a www resource where further information for an object id can be found. The mapping is based on the object namespace
Retrieves annotation for given clone name.
blast Fasta sequence against MAtDB Arabidopsis protein coding genes
Retrieves a basic genetic element by its exact name
returns a collection of AGI_LocusCodes which are somehow related to a given Keyword in their MAtDB annotation (e.g. "wuschel")
retrieves MIPS Arabidopsis Protein Sequence in FASTA format from MAtDB related to a given AGI-Code
retrieves a collection of MIPS Arabidopsis protein sequences related to a given Keyword or AGI-Code from MAtDB (e.g."wuschel", "At2g42410")
returns a collection of EMBL DNA Sequences related to a given AGI-Code/Keyword/EMBL Accession (e.g. "At2g17950","Superman","AJ012310")
Retrieves a list of basic genetic elements with names matching the input string
gets all Links to entries in PlaNet partner databases which refer to the given AGI Locus Code (e.g. At2g17950)
Retrieve annotation for the given genetic element
Retrieves all clone annotation for given search text
retrieves genetic element names related to the given keyword from all MIPS databases (arabidopsis, medicago, maize, rice)
Retrieves the MIPS Arabidopsis Genetic Element Annotation from matdb2 identified by the given name/code/id in GFF3-format
retrieve all genetic elements for given contig as collection of plain-text objects (eg. mth2-11e1)
Wrapper for ATIDB GeneTrap images. From gene report gets GT flanking sequences, parses details page for link to pattern detail page. From each of these, it gets up to 3 images (for 'seedling', 'leaf' and 'mature' patterns). Example Input:AT5G01800.
Retrieves all genetic element names matching given search string (for example all AGI locus codes for search string "At")
Retrieves detailed information including all subelements for a genetic element name from the MIPS PlantsDB.
Retrieves Unspliced sequence for a genetic element name
parses Element Sequences (MIPS PlantsDB) out of any text-xml or text-formatted and gives them back as GenericSequences (output sorted by alphabet)
parses AGI-LocusCodes out of Blast Results or any text-xml or text-formatted (output sorted by alphabet)
Retrieves a list of all genetic elements of a given element type
This service extracts the names of genetic elements from XML documents returned on a query by he MIPS PlantsDB
Retrieves conserved ortholog set (by bbh) for a AGI locus code
blast raw sequence (no special format like FASTA) against MAtDB Arabidopsis protein coding genes
executes blast against MAtDB Arabidopsis protein coding genes
Retrieves Spliced sequence for a genetic element name
Retrieve all genetic elements for given element type
Retrieves Protein sequence for a genetic element name
executes NCBI blast against MAtDB Arabidopsis protein coding genes, returns XML output with a clickable hit graph
returns collection of EMBL Accessions related to a given Keyword (e.g. "superman")
executes NCBI blast against MAtDB Arabidopsis protein coding genes, returns XML output
retrieves pre-calculated TmHMM results for given AGI code
blast raw sequence (no special format like FASTA) against MAtDB Arabidopsis Contigs
Wrapper for the "RIKEN Arabidopsis Phenome Information Database" (RAPID). RAPID line IDs are mapped to AGI codes according to http://rarge.gsc.riken.jp/phenome/?Mode=List. The according line details page is parsed for images and phenotype description. Example input: At3g58650.
retrieves the MIPS Arabidopsis Genetic Element Annotation from MAtDB2 identified by the given name/code/id in GFF format. Guaranteed to retrieve a single entry which is the current up-to-date version
Calculates conserved ortholog sets for a group of organisms. Inputs are the SimapDataset ids for a seed (eg. 14 for arabidopsis) and a group of nonseed genomes (eg. 416, 442 for rice/maize). Calculation is based on Simap.
Returns collection of pubmed ids for a given agi locus code. Based on the literature collection of TAIR (arabidopsis.org).
Retrieves Contigs list for a contig name
This service takes a plant name (ex : AAAA06), or a list of them, and returns full record about phenotype. The service works only with the rice specie (OryzaTagLine namespace).
This service takes a germplasm Id (or plant name, ex : ABAA06), or a list of them, and returns associated FST Id. The service works only with the rice species (OryzaTagLine namespace).
This service takes a FST Id (ex : AAAA06), or a list of them, and returns associated germplasm (plant name). The service works only with the rice specie (OryzaTagLine namespace).
This service takes a germplasm Id (or a plant name, ex : AAAA06), or a list of them, and returns full record about expression. The service works only with the rice specie (OryzaTagLine namespace).
SeedGenesEmbryoImageByAgiCode web service will take an AGI_LocusCode and return a Nomarski microscopy image of an Arabidopsis seed with the embryo at the typical stage that development is arrested for a knock-out mutant at that gene.
IMB get maximally representative cluster details
This service blasts a sequence against the gabi database and returns the Blast-output in XML-format. Blast-parameters are: -v 25 -F T -m 7 -e 0.0000000001 -p blastn.
This service checks if a given identifier is available at the RZPD as clone.
This service extracts the identifiers of subjects from Blast-output in XML-format.
Retrieve available bioinformatics from Chinook
This service will identify Hydrogen bonds occurring in a protein structure. It requires a PDB file. The identification of the H-bonds is a 2-step process: 1. Explicit hydrogen coordinates are calculated. 2. Hydrogen bonds are located, on the basis of a minimal inter-atomic distance between the hydrogen and the acceptor, and on a correct angle between the donor-hydrogen bond and the hydrogen-acceptor pseudo bond. It is possible to locate H-bonds for backbone or side chains only. The service will also propose a rasmol script to visualize the H-bonds identified.
Execute a blast using blastpgp over PDB, a protein structure data base.
Protein simple builder. This will take an amino acid sequence, a sequence of letters describing the conformation of the backbone of each amino acid, and return a PDB file. In its current version, this is a facility to obtain a PDB file to undergo further processing using external tools. A more complete and accurate builder is under construction.
Protein secondary structure identification with STRIDE.
A highly accurate method for protein secondary structure prediction
This implementation of clustalw is restricted to multiple alignment of protein sequences.
NetASA predicts the solvent accessibility of amino acid residues in a protein using a neural network algorithm.
This service allows to generate protein coordinates resulting from side chain subsitutions (backbone unaffected).
A neural network protein secondary structure prediction method
Given a protein sequence, this will run a predictor for the bonding state of its cysteines. It will return a prediction concerning all the cysteines at a while, given the observation that in most proteins, cysteines tend to have the same state (i.e. form or not disulfide bonds).
Mead-pot performs the calculation of the electrostatic potential for a protein by solving the Poisson-Boltzmann equation. It is a server adaptation of the potential program of the MEAD package (Macroscopic Electrostatics with Atomic Detail, D. Bashford). The present version assumes negative charges for GLU, ASP, Cter, and positive charges for ARG, LYS, Nter. Results are displayed on the molecular surface by a color code (red negative, blue positive). Warning: - This service is currently working only for proteins without ions or cofactors, (work in progress). - Work is also in progress to allow user specification of the charges per residue, or the focus on some region of interest).
HCA is a method to detect, from amino acid sequence, periodic occurrence of hydrophobic amino-acids compatible with regular secondary structures. This service will produce a bi-dimensional plot (postscript format), from which such periodicities can be analyzed.
Protein secondary structure identification with P-SEA.
PredAcc is a program to predict the solvent accessibility of the amino-acids of a protein given its amino-acid sequence
Protein amino acid charge calculation as a function of the pH. Warning: this service is not fully functional (see help).
A tool to scan databanks of nucleic acid or amino acid sequences in order to retrieve sequences distantly related to the query.
This service extracts all the beta-turns from a PDB file. It uses the program DSSP to extract helices and strands.
Squizz is a tool for sequence conversion or alignement conversion.
Retrieves NASC ecotypes for a given EMBL accession from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input:X98772 .
Retrieves the name of a stock for a given type of seed from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Single marker.
Retrieves NASC ecotypes for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: salk_000013.
Retrieves the locus for a given EMBL accession from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Y15193.
Retrieves the NASCArrays reference number for a given NASC stock code from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'NW20'.
Retrieves Arabidopsis images for a given allele from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: cer2-1, arc1-1.
Retrieves NASC mutagens for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: salk_000013.
Retrieves Arabidopsis publications for a given NASC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'N500013'.
Retrieves NASCArrays experiment description for a given slide name, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'Durrant_1-1_wild-type_Rep1_ATH1'.
Retrieves the name of a stock for a given ABRC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: CS20.
Retrieves Arabidopsis phenotypes corresponding to the given NASC seed type from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: Single marker.
Retrieves the NASC donor name for a given EMBL accession number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'X98772'.
Retrieves Arabidopsis phenotypes corresponding to the given mutagen from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: NMB
Retrieves the availability of a stock for a donor number given from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'salk_000013'.
Retrieves the Arabidosis allele for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: apetala.
Retrieves the name of a stock for a given keyword from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: trichomes.
Retrieves NASC Stock code for a given EMBL accession from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Y15193.
Retrieves the locus for a given allele from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: aux1-7.
Retrieves the NASC donor surname for a given mutagen from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: EMS.
Retrieves the EMBL accession number for a given Arabidopsis insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: CSHL:ET84.
Retrieves NASC ecotypes for a given NASC stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: NW20.
Retrieves NASCArrays experiment description for a given experiment name, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'Comparison of transcriptional profiles between sni1 and wild type'
Retrieves slide names for a given experiment name from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'FRI FLC combos'.
Retrieves Arabidopsis images for a given NASC donor namefrom the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'Kevin Pyke'.
Retrieves the EMBL accession number for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: AT_111.
Retrieves the NASCArrays reference number for a given NASCArrays experiment name from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'Baseline experiment floral homeotics'.
Retrieves Arabidopsis phenotypes corresponding to the given a donor number (http://arabidopsis.info). Example input: salk_000013
Retrieves the growth requirements for a given NASC stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'eceriferum', 'Landsberg erecta'.
Runs the analysis tool, GeneSwinger for a given Affymetrix probeset ID from the ATH1 chip. (http://affy.arabidopsis.info). Example input: 252056_at.
Retrieves NASC insert numbers for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: salk_000013.
Retrieves Arabidopsis images for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: DP23, L4, 304.
Retrieves NASC Stock code for a given ABRC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: CS20".
Retrieves the name of a stock for a given mutagen from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: NMB.
Retrieves NASC ecotypes for a given insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 083008.
Retrieves the availability of a stock for a given NASC stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'N20', 'N901', 'N960', 'N1150'.
Retrieves NASC_codes for a given AGI locus code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: At1g20310.
Retrieves the NASC donor name(s) for a given ABRC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'CS20', 'CS70', 'CS7'.
Retrieves the name of a stock for a given AGI locus code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'At1g19100'.
Retrieves the name of a stock for a given donor surname from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Relichova.
Retrieves Arabidopsis publications for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'salk_000013'.
Retrieves slide names for a given reference number from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'NASCARRAYS-389'.
Retrieves NASC Stock code for a given locus in Arabidopsis from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: cer5.
Retrieves NASC insert numbers for a given locus from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: At4g22165.
Retrieves donor surname for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'salk_000014'.
Retrieves the NASC donor name for a given NASC stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'N4', 'N933', 'N3074', 'N1150'.
Retrieves the EMBL accession number for a given allele from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: cer5-1.
Retrieves the Arabidosis allele for a given ABRC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: CS20.
Retrieves the locus for a given a stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: N6, N4, N3074.
Retrieves NASC Stock code for a given donor surname from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Plieth.
Retrieves NASC mutagens for a given NASC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: N3074.
Retrieves the description of a stock for a given name of a stock from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'albina', 'ZWILLE'.
Retrieves Arabidopsis phenotypes corresponding to the given Arabidopsis gene symbol from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: cer2
Retrieves Arabidopsis phenotypes corresponding to the given ABRC code from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: CS20.
Retrieves the growth requirements for a given stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'N6', 'N933', 'N20'.
Retrieves the EMBL accession number for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'fah1-7 ttg'.
Retrieves Arabidopsis phenotypes corresponding to the given NASC stock Code from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: NW20
Retrieves NASC mutagens for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: apetala.
Retrieves NASCArrays experiment description for a given MGED experiment design type from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: time_series_design.
Retrieves the growth requirements for a given ABRC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'CS20', 'CS3', 'CS90'.
Retrieves NASC insert numbers for a given ABRC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: CS25583.
Retrieves the expression values for a given Affymetrix ProbeSet ID by Slide name from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'Durrant_1-1_wild-type_Rep1_ATH1'.
Retrieves the name of a stock for a given ecotype name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: S96.
Retrieves the habitat in which Arabidopsis grows for a given stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'N900', 'N901', 'N902', 'N960', 'N1150'.
Retrieves NASC insert numbers for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: AT_111.
Retrieves the images for a given NASC stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: NW77.
Retrieves Arabidopsis phenotypes corresponding to the givenecotype name from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: 'Ag-0'.
Retrieves NASC insert numbers for a given stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: N700001.
Retrieves the EMBL accession number for a given NASC stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: N3574.
Retrieves Arabidopsis phenotypes corresponding to the given keyword from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: David Meinke
Retrieves the name of a stock for a given locus from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: psv.
Retrieves NASC Stock code for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: An-1".
Retrieves NASC inserts for a given AGI locus code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: At1g11900.
Retrieves Arabidopsis seed type for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'salk_000013'.
Retrieves NASC Stock code for a given Keyword from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: dwarf.
Retrieves the description of a stock for a given NASC stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'N500013', 'N3074'.
Retrieves the availability of a stock for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'angustifolia', 'chlorina', 'brevipedicellus', 'agamous'.
Retrieves NASC mutagens for a given from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: X98772.
Retrieves Arabidopsis images for a given Insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'CSHL:ET14'.
Retrieves Arabidopsis images for a given ABRC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: CS30.
Retrieves NASC Stock code for a given ecotype name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Ag-0.
Retrieves the description of a stock for a given insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: '083008'.
Retrieves the Arabidosis allele for a given EMBL accession from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: X98772.
Retrieves NASC Stock code for a given collection name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: CAUT.
Retrieves Arabidopsis seed type for a given insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: launchpad:1A.
Retrieves NASC ecotypes for a given mutagen from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input:EMS .
Retrieves Arabidopsis publications for a given Arabidopsis insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: '083008'.
Retrieves NASC mutagens for a given insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 083008.
Retrieves NASC Stock code for a given allele from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: cer5-1.
Runs the analysis tool, GeneSwinger for a given AGI locus code. (http://affy.arabidopsis.info). Example input: At3g52590.
Retrieves Arabidopsis seed type for a given stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: N3074.
Retrieves the EMBL accession number for a given mutagen from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: gamma rays.
Retrieves the EMBL accession number for a given ABRC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: CS20.
Retrieves the NASC donor name for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'An-1', 'AT_3462', 'chlorina', 'AT_111'.
Retrieves NASCArrays reference number for a given slide name from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'Penfield_1-1_endosperm-control_Rep1_ATH1'.
Retrieves the EMBL accession number for a given keyword from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: trichomes.
Retrieves Arabidopsis images for a given from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Ag-0, Bla-10, Br-0, Fe-1.
Retrieves the name of a stock for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: salk_000014.
Retrieves the name of a stock for a given stock code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: N4, N6, N1654, N933.
Retrieves Arabidopsis phenotypes corresponding to the given allele from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: cer5-1
Retrieves the name of a stock for a given insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 083008.
Retrieves the name of the collection from which the given NASC donor number belongs to from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'salk_000013\.
Retrieves slide names for a given NASC stock ocde from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: N1093.
Retrieves Arabidopsis phenotypes corresponding to the given EMBL accession (http://arabidopsis.info). Example input: X98772
Retrieves Arabidopsis phenotypes corresponding to the given NASC stock name from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input:An-1.
Retrieves the Arabidosis allele for a given locus from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: cer2.
Retrieves the description of a stock for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'salk_000013'.
Retrieves NASC mutagens for a given allele from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: cer5-1.
Retrieves an Arabidopsis Image for a given AGI Locus Code from NASCs Germplasm database (http://arabidopsis.info). Examples include: At4g24510 and At2g26670
Retrieves Arabidopsis publications for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'salk_000013 (O)'.
Retrieves the habitat in which Arabidopsis grows for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'An-1'.
Retrieves the NASC donor surname for a given insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: CSHL:ET84.
Retrieves the name of a stock for a given allele from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Cer-1.
Retrieves the EMBL accession number for a given locus from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: cer2.
Retrieves the Arabidosis allele for a given NASC code from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: N6.
Retrieves NASC Stock codes for a given insert number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 083008.
Retrieves the EMBL accession number for a given seed type from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'Single marker'.
Retrieves Arabidopsis images for a given keyword from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'asymmetric', 'epicuticular wax layer'.
Retrieves the NASC Stock code for a given donor number from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 304.
Retrieves the name of a stock for a given EMBL accession from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Y15193.
Retrieves Arabidopsis phenotypes corresponding to the given donor surname from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: Hobbie
Retrieves the EMBL accession number for a given donor surname from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: Hobbie.
Retrieves NASC mutagens for a given locus from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: cer2.
Retrieves NASCArrays experiment description for a given from NASCArrays reference number from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: NASCARRAYS-136.
Retrieves Arabidopsis phenotypes corresponding to the given AGI locus code from the Nottingham Arabidopsis Stock Centre germplasm database (http://arabidopsis.info). Example input: At1g20300
Retrieves NASC insert numbers for a given EMBL accession from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: AB028622.
Retrieves Arabidopsis phenotypes corresponding to the given insert number from NASCs Germplasm database (http://arabidopsis.info). Example input: 083008
Retrieves Arabidopsis images for a given NASC stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: brevipedicellus, Angustifolia, Dentata.
Retrieves NASC Stock code for a given mutagen from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: NMB".
Retrieves NASCArrays experiment description for a given NASC stock code, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'N1093', 'NW20'
Retrieves Arabidopsis seed type for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: 'root hair defective'.
Runs the analysis tool, GeneSwinger for a given Affymetrix probeset ID from the AG chip. (http://affy.arabidopsis.info). Example input: 13129_f_at.
Retrieves the locus for a given stock name from the Nottingham Arabidopsis Stock Centre Germplasm database (http://arabidopsis.info). Example input: apetala.
Consumes a collection of GO ids and returns a collection of AGI LocusCodes
Consumes an AGI Locus code and retrieves an image of the GFP expression pattern or heatmap for that locus from AREX DB.
This service is currently under development, it is as of now, unreliable at best
This service takes in a String object where the value of the string is the search word and returns a collection of strings of the searched lexicon database
Converts amino acid objects into FastA formatted records, primarily to increase inter-service compatibility
BLAST hardware search service: formats alignment result in NCBI_BLAST_Text format
This service retrieves extracts from a BASE2 database
takes two collections of input objects and returns a collection of output objects representing the non-redundant union of those two collections. Objects are determined to be similar or dissimilar based on their namespace/id pairs, regardless of Object Class; in cases where two identical objects have different Class instantiations, the Class of the object in Collection1 is preferred
takes two collections of input objects and returns a collection of output objects representing the non-redundant intersection of those two collections. Objects are determined to be similar or dissimilar based on their namespace/id pairs, regardless of Object Class; in cases where two identical objects have different Class instantiations, the Class of the object in Collection1 is preferred
It brings back a random image. But a user can influence the choice of the returned image by requesting an image by sending a particular number (unknown numbers are ignored, and a random image is returned).
This is a cult service, known to an exclusive group of persons sharing an esoteric interest. One of their believes is that a word started on January, 1 1970.
Yes, you can unregister this service anytime...
This service extracts the real content of an input text and return it as a primitive String type. The main reason is to show that one can send a more specialized data type to this service (even though the service claims that it operates only on text-plain data type). The service is part of the tutorial and documentation of the Moses system - its source code is distributed with jMoby.
How to say "Hello" in many languages. Heavily based on a web resource "Greetings in more than 800 languages", maintained at http://www.elite.net/~runner/jennifers/hello.htm by Jennifer Runner.
Example service: formats a sequence in FASTA format
Get the scientific name corresponding to GenBank GI
Provide NCBI/EMBL/DDBJ accessions for a word
Get accession of all Mt entries with <keyword> connection
Runs Meta-alignment software on a multiple running mode, receiving a collection of maps, making pairs of them and, foreach pair, producing, in GFF format, alignments of sequences of TF binding sites
Converts aminoacid FASTA sequence into an aminoacid sequence
Produces alignments of sequences of TF binding sites and returns the predictions in GFF format. You can use runMatScanGFF to produce the input GFF files, specifying the 'log-likelihood' matrix mode
Sequence retrieval tool from Ensembl database. It returns the upstream sequence of a given set of Ensembl gene identifiers. These identifiers could be external ones, such as Refseq Ids or Affymetrix ids.
Runs Meta-alignment software on a multiple running mode, receiving a collection of maps, making pairs of them and, foreach pair, producing, in 'Meta-alignment' format, alignments of sequences of TF binding sites
Filters a set of sequences based on their length. Only sequences which length is greater than the length cutoff will be returned. It also filters out the quality data associated with the removed sequences.
Analyzes a DNA sequence for putative transcription factor binding sites from Transfac or Jaspar and reports them in GFF format
Parses the score or probability motif matrices from MEME output
Runs Phrap to Assemble a set of DNA sequences
Phred writes the base calls from a set of chromatograms and returns a set of DNA sequences and FASTA base quality data
Runs dust to mask low-complexity regions within a set of DNA sequences
Converts a FASTA object into a collection of GenericSequence moby objects
Runs RepeatMasker to mask repeat sequences a set of DNA sequences
Ab initio gene prediction tool that returns the gene predictions in GFF format (GFF version 2).
Plasmodium falciparum (malaria parasite)
Converts a generic sequence into a FASTA sequence
Converts aminoacid FASTA sequences into a collection of aminoacid sequences
Runs Phrap to Assemble a set of DNA sequences, taking into account base quality data
Parses a collection of meta-alignment outputs to produce a sequence similarity score matrix
Runs Multiple-Meta-Alignment software to perform multiple non-collinear transcription factor map alignments of promoter regions. It returns the multiple-meta-alignment output in meta-alignment text format.
Filters a set of sequences based on their length. Only sequences which length is greater than the length cutoff will be returned.
Ab initio gene prediction service that runs geneid with synteny evidences and returns the output predictions in GFF format. To generate the synteny evidences, use a tblastx service
Analyzes a set of protein or DNA sequences for similarities among them and produces a description (motif) for each pattern it discovers. The results are returned in HTML format
background markov model training (value is the model order)
Sequence retrieval tool from Ensembl database. It returns the upstream sequence of all orthologues of a given Ensembl gene identifier. The identifier could be an external one, such as a Refseq Id or an Affymetrix id.
Runs Multiple-Meta-Alignment software to perform multiple non-collinear transcription factor map alignments of promoter regions. It returns the multiple-meta-alignment output in GFF format.
Parses a collection of meta-alignment outputs to produce a text-formatted sequence similarity score matrix
Run RepeatMasker to mask repeat sequences within a DNA sequence
Converts a DNA FASTA sequence into a DNA sequence
Translates the GeneID gene predictions, given in GFF format, into a set of aminoacid sequences
Phred writes the base calls from a chromatogram and returns a DNA sequence and FASTA base quality data
Runs gff2ps software to vizualize a set of GFF annotations maps. It returns an encoded image in JPEG format.
Ab initio gene prediction tool that returns the gene predictions in GFF format (GFF version 3). It also returns a set of translated aminoacid sequences.
Converts a collection of generic sequences into FASTA sequences
Produces alignments of sequences of TF binding sites and returns the predictions in 'Meta-alignment' format. You can use runMatScanGFF to produce the input GFF files, specifying the 'log-likelihood' matrix mode.
Runs cluster v3.0 to that implements k-means algorithm to cluster genes together. The input is a gene score matrix represented as a MicroArrayData_Text object.
Analyzes a collection of DNA sequences for putative motifs (transcription or splicing factor binding sites) and reports them in GFF format. The collection of motifs is given by the user as a set of Position Weight Matrices (PWMs)
Runs dust to mask low-complexity regions within a DNA sequence
Runs cross_match to screen out vector sequences from a set of DNA sequences. The vector sequences dataset is stored internally
Analyzes a set of protein or DNA sequences for similarities among them and produces a description (motif) for each pattern it discovers. The results are returned in MEME text format
Runs cross_match to screen out vector sequences from a DNA sequence. The vector sequences dataset is stored internally
Converts DNA FASTA sequences into a collection of DNA sequences
Analyzes a collection of DNA sequences for putative transcription factor binding sites from Transfac or Jaspar and reports them in GFF format
Runs dust to mask low-complexity regions within a set of DNA sequences in FASTA format
Retrieves PubMedCentral Ids i.e. literature for given Arabidopsis AGI Locus codes.
Takes a collection of numbers and performs the specified operation. Operations are specified by secondary parameters; for example +, avg.
Returns zero or more CDD, Conserved Domain DB, identifiers given a short non-unique label. This service utilizes SHoundGetDomainIdFromLabel (www.blueprint.org).
Fetches LocusLink IDs (LocusID) for a list of given protein sequences.
Fetches all Gene Ontology (GO) term identifiers assigned to a list of protein sequences. Uses redundancy information for the query GI identifiers. This means that if the query fails for the input GI identifier, then the query will be retried for all other GI identifiers that belong to the same redundant group. An individual sequence can be referred to by one or more a process, function or component terms.
This services consumes a FASTA object containing multiple records, along with a collection of ID numbers in any namespace. The service returns those sequences whose records contain an extract match to those ID numbers passed in as input.
Fetches protein sequences on which a domain from the Conserved Domain Database (CDD) was identified by Reverse Position Specific BLAST. The function uses an E-value cutoff for reporting results. This service utilizes SHoundGetGisByDomainId (www.blueprint.org).
Fetches LocusLink IDs (LocusID) for a given Online Mendelian Inheritance in Man (OMIM) ID.
Retrieves a list of protein BLAST neighbours possessing 3-D structure. Uses redundancy information for the query protein. The BLAST protein neighbours were calculated using 0.01 maximum E-value cutoff.
This service takes as input a KEGG pathway and KEGG ids. It then proceeds to use the KEGG utilities to highlight the ids on the pathway and return that image to you.
Fetches identifiers about domains from the Conserved Domain Database (CDD) as assigned by Reverse Position Specific BLAST to a given protein sequence. Uses redundancy information for the query proteins. This means that if the query fails for the input GI identifier, then the query will be retried for all other GI identifiers that belong to the same redundant group. This service utilizes SHoundGetDomainsFromGi (www.blueprint.org).
This service consumes a variety of different identifiers, does a SeqHound retrieval of the appropriate sequence object, and outputs it as a GFF object.
Operates on Gene Ontology (GO) vocabulary graphs. Reports if a given GO identifier describes a cellular process, a cellular function or a cellular component.
Operates on Gene Ontology (GO) vocabulary graphs. Retrieves a list of processes, functions or components situated directly above a given GO identifier in the graphs. NOTE: due to the logic of the GO hierarchy graphs, it is possible that a GO identifier will have more than one parent
This service consumes an identifier under the Swiss-Prot / UniProt namespace. Using the input identifier, relevant snp data is returned.
takes a keyword as input and returns a collection of GO terms that are associated with that keyword
This service, given a KEGG pathway, returns a Gif image of the pathway if it exists. For example, the <Object, KEGG_PATHWAY, 'hsa00053') returns a diagram of the pathway 'ASCORBATE AND ALDRATE METABOLISM'.
Gets uniprot identifiers by keyword using the bfind utility via the KEGG soap API
takes a GO term id and retrieves a collection response of all gene products annotated to that ontology term.
consumes a NCBI_Acc, NCBI_gi, PIR, SwissProt, Embl, or PDB identifier and returns the equivalent genbank record as a DNA, RNA, AminoAcid sequence object as appropriate
Fetches all Gene Ontology (GO) term identifiers assigned to a protein sequence. Uses redundancy information for the query GI identifier. This means that if the query fails for the input GI identifier, then the query will be retried for all other GI identifiers that belong to the same redundant group. An individual sequence can be referred to by one or more a process, function or component terms.
This service, given a KEGG identifier, attempts to retrieve KEGG pathways that that contain this ID. For example, passing in: hsa:6402 results in the following pathway returned: hsa04514.
Retrieves collection of GI numbers representing a non-redundant set of all genbank genomic DNA entries for the genome identified by that taxon identifier
consumes a NCBI_Acc, NCBI_gi, PIR, SwissProt, Embl, or PDB identifier and returns the equivalent genbank record as a VirtualSequence object (i.e. only the sequence length)
Fetches LocusLink IDs (LocusID) for a given protein sequence.
Returns a short non-unique label given a domain for a CDD, SMART, or COGs. The labels are preferred amongst the scientific community. This service utilizes SHoundGetDomainLabelFromDomainId (www.blueprint.org).
Fetches all protein sequences which were assigned a list of Gene Ontology (GO) functions, processes or components. Currently 25 hits are returned, but you can adjust that number as you see fit.
consumes a NCBI_Acc, NCBI_gi, PIR, SwissProt, Embl, or PDB identifier and returns the equivalent genbank record as a genbank-flatfile object
Operates on Gene Ontology (GO) vocabulary graphs. Retrieves a list all of processes, functions or components situated below a given GO identifier in the graphs.
wraps the SeqHound SHoundGetTaxParent function. Takes an NCBI taxon ID and returns the taxon ID of the parent taxonomic node
Returns zero or more Pfam, Pfam-A seed alignments from the Protein families database of alignments and HMMs, identifiers given a short non-unique label. This service utilizes SHoundGetDomainIdFromLabel (www.blueprint.org).
This service takes in a gene name, as an identifier, and returns a collection of possible UNIPROT identifiers that may (or may not) describe that gene. This service utilizes the bfind (KEGG) to get hits.
Genomes that gene identifiers are searched over.
takes an NCBI taxon ID and returns a collection of taxon id's that are children of this node in the taxonomic hierarchy
Fetches all Gene Ontology (GO) IDs assigned to a protein sequence. An individual sequence can be referred to by one or more process, function or component terms.
Fetches LocusLink IDs (LLID) for a given Conserved Domain Database (CDD) ID
Fetches all Gene Ontology (GO) IDs assigned to a list of protein sequences. An individual sequence can be referred to by one or more process, function or component terms.
Fetches all Gene Ontology (GO) IDs for a given LocusLink ID (LLID)
Operates on Gene Ontology (GO) vocabulary graphs. Retrieves a name of a process, a function or a component for a given GO identifier.
Returns zero or more COGs, Clusters of Orthologous Groups of proteins, identifiers given a short non-unique label. This service utilizes SHoundGetDomainIdFromLabel (www.blueprint.org).
Consumes MOBY Simple outputs of any type and extracts the CrossReferences of the primary object as a collection of MOBY Objects in whatever namespace they are in.
Converson of MOBY Generic Sequence objects to FASTA objects
This function operates on Gene Ontology (GO) vocabulary graphs. It retrieves a list of processes, functions or components situated directly above a given GO identifier in the graphs.
This service consumes EMBL accessions and converts them to genbank gi numbers using Seq Hound's SHoundFindAcc method
This service consumes an identifier from the following namespaces: NCBI_gi, GenBank, UniProt, UniGene, PMID or OMIM and returns a KEGG identifier that represents the KEGG id mapped to the input identifier. An example input would be (in <Object, ns, id> triple format, <Object, omim, 153240>
This service consumes the HTML that comes from the GeneMark HMM CGI server at gatech and extracts the protein sequences in fasta format if they exist. the CGI should be run with protein = 1 as a parameter. The GeneMarkHMM_Arabidopsis service is designed to feed into this parser by default.
consumes a NCBI_Acc, NCBI_gi, PIR, SwissProt, Embl, or PDB identifier and returns the equivalent genbank record as a FASTA object
Gets the uniprot identifier and description from a keyword using the bfind utility courtesy of KEGG.
This function operates on Gene Ontology (GO) vocabulary graphs. It retrieves a list of processes, functions or components situated directly below a given GO identifier in the graphs.
Fetches all Pfam IDs from the Conserved Domain Database (CDD) for a given LocusLink ID (LLID), using SHoundCDDIDFromLLID.
This function operates on Gene Ontology (GO) vocabulary graphs. It retrieves a list of all processes, functions or components situated above a given GO identifier in the graphs.
Fetches all protein sequences which were assigned a list of Gene Ontology (GO) functions, processes or components and evidence code (ECode). Currently 25 hits are returned, but you can adjust that number as you see fit.
This service consumes a FASTA formatted sequence (FASTA or child object) and converts it into a child of Generic Sequence based on the type of sequence in the FATSA file. This is guessed using the BioPerl _guess_alphabet subroutine. The output is either a DNASequence, RNASequence, or AminoAcidSequence object, as appropriate.
Retrieves collection of GI numbers representing a non-redundant set of all genbank Protein entries for the genome identified by that taxon identifier. Only works for completed genomes
Retrieves collection of GI numbers representing all genbank protein entries for the given taxon identifier
Fetches all protein GI identifiers associated with a list of entries in Online Mendelian Inheritance in Man (OMIM) database.
This service consumes an identifier under the EntrezGene_ID / EntrezGene_EntrezGeneID namespaces. Using the input identifier, any relevant gene information is returned regarding that particular gene id.
Consumes a Genetic Map object and converts it to a simple 7-column GFF format object
Consumes a GFF file and renders it to a PNG image
Gets PMID list from GI identifier and Gene Ontology ID (GOID)
This service takes in an annotated jpeg image and returns just the image.
Fetches all protein GI identifiers associated with an entry in Online Mendelian Inheritance in Man (OMIM) database.
takes an NCBI taxon ID and returns the scientific name for the organism represented by that taxon id in NCBI's taxonomy.
Fetches protein GI identifiers associated with NCBI's LocusLink ID (LocusID)
Fetches all CDD IDs from the Conserved Domain Database (CDD) for a given LocusLink ID (LLID), using SHoundCDDIDFromLLID.
Retrieves a collection of protein BLAST neighbours. Uses redundancy information for the query protein. The BLAST protein neighbours were calculated using 0.01 maximum E-value cutoff.
takes a Gene Ontology accession number and returns the term name and definition as a GO_Term object
Retrieves collection of GI numbers representing all genbank DNA entries for the given taxon identifier
Returns zero or more SMART, the Simple Modular Architecture Research Tool, identifiers given a short non-unique label. This service utilizes SHoundGetDomainIdFromLabel (www.blueprint.org).
Retrieves a list of genotype and allele frequencies for non-synonymous SNPs genotyped by HapMap (www.hapmap.org) from the snp input identifier.
This service, given a KEGG pathway, searches for all known genes on that pathway.
Fetches protein GI identifiers associated with a list of NCBI's LocusLink IDs (LocusID).
This service consumes an identifier under the NCBI_dbSNP namespace. The identifier is then converted into an EntrezGene_ID
Gets evidence code from GI identifier and Gene Ontology (GO) ID.
Operates on Gene Ontology (GO) vocabulary graphs. Retrieves a list of processes, functions or components situated directly below a given GO identifier in the graphs.
Fetches all COG IDs from the Conserved Domain Database (CDD) for a given LocusLink ID (LLID), using SHoundCDDIDFromLLID.
Gets a list of Gene Ontology (GO) IDs with a specified GO reference type (e.g. EC).
This service is a wrapper around the GeneMark.hmm CGI interface provided by opal.biology.gatech.edu. It uses the Arabidopsis models as the default, and cannot be reconfigured. The service consumes FASTA and provides the HTML output from the GeneMark.hmm website as its output.
Fetches all protein sequences which were assigned a Gene Ontology (GO) functions, processes or components and evidence code (ECode). Currently 25 hits are returned, but you can adjust that number as you see fit.
Fetches all SMART IDs from the Conserved Domain Database (CDD) for a given LocusLink ID (LLID), using SHoundCDDIDFromLLID.
Fetches all protein sequences which were assigned a given Gene Ontology (GO) function, process or component. Currently 25 hits are returned, but you can adjust that number as you see fit.
Fetches LocusLink IDs (LocusID) for a given Gene Ontology ID (GOID) and evidence code (ECode)
This service consumes an identifier under the KEGG namespace. This identifier is then 'transformed' into a corresponding swissprot/uniprot identifier.
Retrieves assigned TF family name according to the AGRIS dataset for a given AGI locus code (sample input: At1g01010).
Gets a detailed occurrence record from a brief record.
This service brings up a list of taxa that are inmediate lower taxa to the given taxon.
Get taxon ocurrences from GBIF taxon Id.
GBIF service for retrieval of taxon concepts
Get Probe ID in RED by using KOME Gene ID.
Get expression data on a probe derived from microarray experiment.
Get image data to show the positions of probes on transcriptional unit.
Get characteristics of gene in KOME database.
Blast search against transcriptional unit database.
Returns current gene symbol for a given RGD ID
searches RGD Gene list using supplied Keyword
Takes NCBI Acc and returns RGD ID of matching gene record
Returns PMIDs (literature citations) for a given object in RGD (RGD ID)
Returns Genbank nucleotide records (NCBI_Acc) for a given RGD object (RGD ID)
takes the RGD ID of a gene (eg RGD:3889 or 3889) and returns GO IDs for GO annotations to that gene
Returns the SwissProt ID for a given object in RGD given an RGD ID
takes a LocusLink ID of a gene and returns the corresponding Rat Genome Database (RGD) ID
Returns Genbank protein accessions for a given RGD gene record (RGD ID)
consumes a Gene Ontology accession number and returns a collection of associated Pathbase accession numbers.
retrieve DiseaseAreaNameList currently in use in HGVbase
retrieve OligoRoleList currently in use in HGVbase
retrieve ExperimentTypeList currently in use in HGVbase
retrieve SamplepanelSourceOfDNAList currently in use in HGVbase
retrieve CategoryNameList currently in use in HGVbase
retrieve AssayTypeList currently in use in HGVbase
retrieve GenotypedefTypeList currently in use in HGVbase
retrieve CompositionTypeList currently in use in HGVbase
retrieve AssayMethodList currently in use in HGVbase
Run MEME to find common motifs in a collection of two or more sequences
Retrieves a RNA sequence from the PlantsP database (proteins related to phosphorylation, transporters and ubiquitin)
Retrieves a protein sequence from the PlantsP database (proteins related to phosphorylation, transporters and ubiquitin)
Retrieves a DNA sequence from the PlantsP database (proteins related to phosphorylation, transporters and ubiquitin)
Converts a GenericSequence or better to a FASTA
uses the Parablast server at the University of Calgary Sun Centre of Excellence to execute a blastn against the genbank nt database with default parameters.
returns a table of allelic frequencies ordered by marker-type and locus from a list of accessions
takes a locus identifier as input and returns sequence.
takes accession and locus and returns matrix with alleles
Takes a name or an id of genotypeStudy, a name or an id of dna sample and a name or an id of marker and returns a list of alleles
takes a locus or QTL identifier with a possibility of wildcard as input ('locus' or 'qtl' must be specified in the secondary input) and returns a collection of locus or QTL identifiers.
Takes a name or an id of genotype study and returns a list of markers
takes a trait term as input (in a GCP_SimpleIdentifier id) and returns a collection of QTL identifiers annotated with this ontology as output
takes accession in input and returns information about marker types and locus
Takes a name of species and returns a list of genotype studies
Takes a collection dna sample and returns a collection of germplasm
takes a map identifier with a possibility of wildcard as input and returns a collection of matching map identifiers.
takes a collection of accession, and markers to produce a matrix with accession, locus and allelles
Takes a map identifier as input and return details on this map (including map features, length...)
takes a locus or QTL identifier as input ('locus' or 'qtl' must be specified in the secondary input) and returns details for each locus or QTL.
Takes a name or an id of genotype study and returns a list of dna samples
Enter the EntrezGene ID (ie. 5211 for gene pfkl - phosphofructokinase, liver) to lretrieve list of references and abstracts of publications related to the gene of your interest.
This service consumes an identifier under the EntrezGene_EntrezGeneID / EntrezGene_ID namespaces. This identifier is then used to query for any associated GO_Terms.
RPS-BLAST (Reverse PSI-BLAST) searches a query sequence against a database of profiles.
Evaluation of an alignment using Tcoffee.
ClustalW multiple sequence alignments (full method).
Compares a protein sequence against a protein database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
Multiple sequence alignment usinf T-coffee.
Searches a HMM profile database (Pfam) with a query sequence. Use this if you are trying to annotate an unknown sequence.
Makes a profile alignment using Tcoffee.
Searches a set of sequences with a HMM profile.
It constructs a Hidden Markov Model from a multiple sequence alignment.
ClustalW multiple sequence alignments (fast method).
A MOBY service that accepts a taxon name (the full name of a species) and return the list of geographical coordinates where such species was collected. An example of input name is: Vicia faba (which is is a species of bean (Fabaceae) native to north Africa and southwest Asia, and extensively cultivated elsewhere.) The service has also a paging mechanism: a client can ask either all results in one call, or ask to get separate results (see secondary inputs for paging).
Results can be separated into "pages" and a service can return only some of them. The "startPage" specifies a number of the first page (to be returned). Default is zero, meaning "start from the beginning".
Results can be separated into "pages" and a service can return only some of them. The "maxPage" specifies maximum number of returned pages (the real number may be smaller, however). Default is zero, meaning "return maximum number of results".
returns the gene insertions by AGI locus code plus flanking sequence of specified length either side in GFF format
takes a sequence and returns the results of a primer3 search
takes an AGI locus code and returns a collection of relevant Pubmed reference IDs where available
returns an NASC_Code corresponding to the given ATH_Insert_number
takes an AGI code and returns a collection of InterProScanResult objects
returns transcript sequence(s) given an AGI locus code
returns the names of gene insertions by AGI locus code
takes a GFF object specifying a chromosome segment and returns the DNASequence of that segment
returns the sequence identified by the input transcript code
takes an AGI LocusCode and returns a list of synonyms
takes an AGI_TranscriptCode and returns a TargetP_result
returns the codes identifying transcripts belonging to the AGI locus code
returns the names of AGI locus codes by GO accession number
takes an AGI code and returns a collection of GO accession numbers
takes an AGI code and returns a collection of GO terms
returns the gene insertions by AGI locus code in GFF format
returns an ABRC_Code corresponding to the given ATH_Insert_number
Interactions as determined by Giot et al.
Protein-protein interactions using spoke model (direct bait-prey interactions only), by Gavin et al.
Pairs of genes whose expression profiles are correlated at a significance level of p=0.05 or better (lower = better).
Protein-protein interactions supported by a least one co-occurrence in literature, as included in work of Rual et al. (2005).
Transcriptional regulation, as determined by Lee et al. (2002)
Protein-protein nteractions, determined using yeast two-hybrid technique, by Ito et al.(2001)
Pairs of genes whose expression profiles are correlated at a significance level of p=0.05 or better.
Global mapping of yeast genetic interaction network, by Tong et al. (2004)
Protein-protein interactions, by yeast two-hybrid, Stelzl et al. (2005).
Transcription factor targets, as determined by Harbison et al (2003). Grown in rich media, p-value=1e-4.
Protein-protein interactions, by Uetz et al. (2000)
Gene pairs whose expression is correlated at R >= 0.7, in the Cho et al. (1998) cell cycle dataset.
Protein-protein interaction determined by yeast two-hybrid techniques, with post-verification, by Rual et al. (2005).
GEne Prediction Evaluation TOol:Compare two gff files
BioMOBY interface of EMBOSS equicktandem. Finds tandem repeats. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/equicktandem.html
Search a nucleotide fasta sequence against a library of covariance models. Documentation Available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/learn/doc/RnaScan.html
BioMOBY interface of EMBOSS pepcoil. Predicts coiled coil regions. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/pepcoil.html
BioMOBY interface of EMBOSS getorf. Finds and extracts open reading frames (ORFs) . Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/getorf.html
Scan upstream sequence database with an HMM using ehmmsearch. Documentation available at http://emboss.sourceforge.net/embassy/hmmer/ehmmsearch.html
BioMOBY interface of EMBOSS prettyplot. Displays aligned sequences, with colouring and boxing . Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/prettyplot.html
Converts MotifSampler GFF ouput into a collection of nucleic multi-fasta entries corresponding to each motif detected.
Get CDS sequences for a list of gene accession codes. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/carrere/doc/GetCDSSequence.html
BioMOBY interface of EMBOSS sigcleave. Reports protein signal cleavage sites. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/sigcleave.html
BioMOBY interface of EMBOSS pepstats. Protein statistics. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/pepstats.html
This program converts an MSF file into a psi-blast formatted file for -B option use.
This service converts a list (coma, semi-colon, \n separated lines) to a collection of objects.
BioMOBY interface of EMBOSS pepwindow. Displays protein hydropathy. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/pepwindow.html
Overtype a FASTA (generic FASTA sequence) into a FASTA_NA_multi (multiple entries nucleic FASTA sequence) moby class object
BioMOBY interface of EMBOSS oddcomp. Finds protein sequence regions with a biased composition . Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/oddcomp.html
BioMOBY interface of EMBOSS plotorf. Plot potential open reading frames. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/plotorf.html
BioMOBY interface of EMBOSS garnier. Predicts protein secondary structure. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/garnier.html
Build a hidden Markov model from an alignment. Documentation available at http://emboss.sourceforge.net/apps/ehmmbuild.html
BioMOBY interface of EMBOSS freak. Residue/base frequency plot and report. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/freak.html
Retrieve phylogenetic profiles in a tabulated format. Available query species are :Sinorhizobium meliloti str.1021 (SMabc codes),Ralstonia solanacearum GMI1000 (RS0 codes),Xanthomonas campestris pv.campestris (XCC codes). Documentation available at http://bioinfo.genopole-toulouse.prd.fr/comparative/bcg/PhyloPro/index.html
BioMOBY interface of EMBOSS compseq. Counts the composition of dimer/trimer/etc words in a sequence. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/compseq.html
Extract FASTA sequences (gene, cds, utr5/3 or proteins) of the given IMGA_Accession.
Multiple EM for Motif Elicitation Version 3.0 configured for nucleic analysis. Discover motifs shared by a group of sequences. Documentaion available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/carrere/doc/meme/meme-intro.html
BioMOBY interface of EMBOSS iep. Calculates the isoelectric point of a protein. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/iep.html
BioMOBY interface of EMBOSS einverted. Finds DNA inverted repeats. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/einverted.html
Overtype a FASTA (generic FASTA sequence) into a FASTA_NA (nucleic FASTA sequence) moby class object
Multiple alignment from a multifasta file. Default parameters are those used for proteic alignment. Documentation available at http://www.toulouse.inra.fr/multalin/help.html
BioMOBY interface of EMBOSS emowse. Protein identification by mass spectrometry. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/emowse.html
BioMOBY interface of EMBOSS etandem. Looks for tandem repeats in a nucleotide sequence . Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/etandem.html
BioMOBY interface of EMBOSS prettyseq. Output sequence with translated ranges. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/prettyseq.html
Execute a Psi-blast (blastpgp) of an alignment (-B option) against a database (default:Swiss-Prot + TrEMBL). Documentation Available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/dev/carrere/doc/PsiBlastFromAlignment.html
Extract IMGA TigrXML entries from a keyword targeted to description fields.
Multiple EM for Motif Elicitation Version 3.0 configured for proteic analysis. Discover motifs shared by a group of sequences. Documentaion available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/carrere/doc/meme/meme-intro.html
Overtype a FASTA (generic FASTA sequence) into a FASTA_AA_multi (multiple entries proteic FASTA sequence) moby class object
Execute a profile-scan (pftools) against HAMAP profiles database (http://www.expasy.org/sprot/hamap/) and build a swissprot flatfile using matching HAMAP family description, gene name .... Documentation Available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/carrere/doc/ScanHamapFamilies.html
Split an InterProScan result file in raw format into a collection of moby:InterProScanResult objects.
Get upstream region (1000nt before ATG - 1500nt for Medicago truncatula) for a list of gene accession codes. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/carrere/doc/GetUpstreamSequence.html
BioMOBY interface of EMBOSS backtranseq. Back translate a protein sequence. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/backtranseq.html
Get protein sequences for a list of gene accession codes. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/carrere/doc/GetProteinSequence.html
Given a Multi-Fasta file, run seqlogo and return a PNG file. Documentation available at http://weblogo.berkeley.edu/
This program converts an MSF file into a FASTA formatted file.
BioMOBY interface of EMBOSS cusp. Create a codon usage table. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/cusp.html
BioMOBY interface of EMBOSS marscan. Finds MAR/SAR sites in nucleic sequences. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/marscan.html
BioMOBY interface of EMBOSS digest. Protein proteolytic enzyme or reagent cleavage digest.. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/digest.html
BioMOBY interface of EMBOSS hmoment. Hydrophobic moment calculation. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/hmoment.html
Splits a multi-fasta proteic file to produce a collection of proteic single fasta files
BioMOBY interface of EMBOSS cai. CAI codon adaptation index. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/cai.html
Multiple alignment from a collection of fasta files using ClustalW 1.83. Default parameters are those used for proteic alignment. Documentation available at http://www.ebi.ac.uk/clustalw/
BioMOBY interface of EMBOSS pepnet. Displays proteins as a helical net. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/pepnet.html
Retrieve HAMAP family entry from database (http://www.expasy.org/sprot/hamap/). Documentation Available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/carrere/doc/GetHamapFamily.html
Execute a TBlastN against a database of Plants EST. Documentation Available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/carrere/doc/TBlastNPlantsEST.html
Converts iprscan output into a description using Swiss-Prot format.
BioMOBY interface of EMBOSS helixturnhelix. Report nucleic acid binding motifs. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/helixturnhelix.html
Get the MENS EST Cluster expression pattern from a given list of IMGA identifier
BioMOBY interface of EMBOSS palindrome. Looks for inverted repeats in a nucleotide sequence . Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/palindrome.html
Overtype a FASTA (generic FASTA sequence) into a FASTA_AA (proteic FASTA sequence) moby class object
BioMOBY interface of EMBOSS pepwheel. Shows protein sequences as helices. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/pepwheel.html
Execute a Blastp against Imga proteic database (Medicago truncatula).
BioMOBY interface of EMBOSS chips. Codon usage statistics. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/chips.html
Given a Multi-Fasta file, run MotifSampler with default parameters. (-s 1 p 0.5 -M 0 -n 1 -w 8 -x 1 -r 1). More information on MotifSampler program at http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html
BioMOBY interface of EMBOSS codcmp. Codon usage table comparison. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/codcmp.html
BioMOBY interface of EMBOSS charge. Protein charge plot. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/charge.html
BioMOBY interface of EMBOSS checktrans. Reports STOP codons and ORF statistics of a protein. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/checktrans.html
Multiple alignment from a collection of fasta files. Default parameters are those used for proteic alignment. Documentaion available at http://www.toulouse.inra.fr/multalin/help.html
Multiple alignment from a multifasta file using ClustalW 1.83. Default parameters are those used for proteic alignment. Documentation available at http://www.ebi.ac.uk/clustalw/
BioMOBY interface of EMBOSS tmap. Displays membrane spanning regions. Documentation available at http://bioinfo.genopole-toulouse.prd.fr/services/biomobylipm/services/prod/emboss/doc/tmap.html
This service receives as input a DNA sequence, an integer parameter indicating the maximum number of acceptable mismatches, the length value representing the minimum match length and arabidopsis index to search (Valid values are: ATexon and ATgene). Using Vmatch, a versatile software tool for efficiently solving large scale sequence matching tasks (http://www.vmatch.de/), the sequence is "matched" against the selected arabidopsis index and returns the list of "matches" (i.e. locations) in BasicGFFSequenceFeature objects. Seed length is set to 8. Important note: results limited to MAX_RESULTS (currently set to 750)
DIALIGN is a software program for multiple alignment developed by Burkhard Morgenstern et al. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences. No gap penalty is used. This approach is especially efficient where sequences are not globally related but share only local similarities, as is the case with genomic DNA and with many protein families.
RNA folding based on abstract shapes. This is the standard mode of operation when no other options are given. It calculates the shapes and the corresponding shreps based on free energy minimization.
1.leastAbstract, 2.intermediateAbstraction, 3.intermediateAbstraction,4.intermediateAbstraction
DIALIGN is a novel alignment program based on segment-to-segment comparison.It is especially suited to detect local similarities among distantly related sequences.
Produzir como resultado um arquivo fasta.
look up the consensis sequence for an SGN unigene, given an SGN-U number
Takes an SGN EST ID and returns unigene data.
Retrieves the Locus for the associated Antirrhinum(snapdragon) allele.
Consumes DragonDB allele identifiers and returns a collection of images of plants homozygous for that allele
A keyword is entered as a Global_Keyword namespace, wildcards are appended before and after the keyword, then this string is used to search the descriptions of all mutant phenotypes in the DragonDB database. Matching phenotypes are then traced back to the affected locus name, and a collection of Objects in the DragonDB_Gene namespace (Locus names) are returned in response
Retrieves collection of Antirrhinum alleles for a given keyword by matching against the phenotypic description. wildcards are automatically added as '* keyword *'
Consumes an id representing a DragonDB Sequence (Snapdragon; (Antirrhinum majus) and returns an identifier representing a DragonDB genetic map.
Retrieves collection of Antirrhinum alleles for a given Locus
This service returns GeneticMap objects representing the mapped loci from the DragonDB (Snapdragon/Antirrhinum majus) genome database. Maps are retrieved by their DragonDB_MapIDs
Retrieves the Locus for the associated Antirrhinum(snapdragon) Sequence ID.
This service consumes an allele identifier in the DragonDB_Allele namespace and retrieves the allele phenotypic description from the Antirrhinum majus (Snapdragon) DragonDB database.
Perform blast analysis against the Dragon database at antirrhinum.net.
A service that takes in as input blast text from a blast against DragonDB, then parses out the subject id's of hits and returns them as a collection.
High-throughput search of SNPs with potential phenotypic effect at transcriptional level