Franck Tanoh (28 days ago)
Genome Information Broker for Viruses (GIB-V) is a complete virus genome data repository. Use this service to query the GIB-V database.
SOAP variant: http://www.biocatalogue.org/services/19
Franck Tanoh
Profile
Display Name:
Franck Tanoh
Email address:
ytanoh [at] cs.man.ac.uk
Affiliation:
University of Manchester
Country:
United Kingdom
Services Submitted (106)
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 25
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Annotations: 3
 0
3
 0
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by Franck Tanoh (28 days ago)
Franck Tanoh (28 days ago) |
Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
Base URL:
http://xml.nig.ac.jp/rest/Invoke?service=GIBV |
8 REST Endpoints
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40
0
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Annotations: 5
0
5
0
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by Franck Tanoh (about 1 month ago)
Franck Tanoh (about 1 month ago)
"GTPS" is acronym of Gene Trek in Procaryote Space. Various complete genomes of eubacteria and archaea have been registered in the International Nucleotide Sequence Databases (INSD) of DDBJ/EMBL/GenBank. The annotation and sequence data are available from GIB (Genome Information Broker; http://gib.genes.nig.ac.jp/).
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
Base URL:
http://xml.nig.ac.jp/rest/Invoke?service=GTPS |
8 REST Endpoints
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69
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Annotations: 6
0
6
0
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by Franck Tanoh (about 1 month ago)
Franck Tanoh (about 1 month ago)
RESTful interface to search and retrieve data from the Protein Data Bank (PDB). The Protein Data Bank is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.
website: http://www.pdb.org/pdb
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Provider:
Protein Data Bank, USA (RCSB PDB)
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Submitter / Source:
Base URL:
http://www.pdb.org/pdb/rest |
8 REST Endpoints
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25
0
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aka
knotInframe
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Annotations: 16
5
11
0
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by Franck Tanoh (2 months ago)
Franck Tanoh (2 months ago)
KnotInFrame is a pipeline to predict ribosomal -1 frameshift sites with a simple pseudoknot as secondary structure in DNA and RNA sequences. The prediction is based on a comparison between the minimal free energy (mfe) structure calculated by RNAfold ( http://www.tbi.univie.ac.at/~ivo/RNA/ ) from the Vienna package and the mfe-structure computed by a modified version of pknotsRG-mfe, called pknotsRG-frameshift developed by J. Reeder/R.Giegerich.
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Provider:
Bielefeld University
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Submitter / Source:
WSDL Location:
http://bibiserv.techfak.uni-bielefeld.de/wsdl/knotinframe.wsdl |
2 SOAP Operations
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65
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Annotations: 4
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4
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by Franck Tanoh (2 months ago)
Franck Tanoh (2 months ago)
GTOP is a database built by the Laboratory of Gene-product Informatics at the National Institute of Genetics consisting of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures.
SOAP variant: http://www.biocatalogue.org/services/17
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
Base URL:
http://xml.nig.ac.jp/rest/Invoke?service=Gtop |
3 REST Endpoints
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56
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Annotations: 6
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6
0
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by Franck Tanoh (2 months ago)
Franck Tanoh (2 months ago)
GIB (Genome Information Broker) is the comprehensive data repository of complete microbial genomes in the public domain. The service allows you to retrieve data (accession, organism, CDS etc) from GIB.
SOAP variant: http://www.biocatalogue.org/services/16
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
Base URL:
http://xml.nig.ac.jp/rest/Invoke?service=Gib |
11 REST Endpoints
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70
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Annotations: 6
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6
0
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by Franck Tanoh (2 months ago)
Franck Tanoh (2 months ago)
Finds regions of similarity between biological sequences by executing BLAST with program, database, a query sequence and options.
SOAP variant: http://www.biocatalogue.org/services/8
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
Base URL:
http://xml.nig.ac.jp/rest/Invoke?service=Blast |
2 REST Endpoints
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45
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Annotations: 6
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6
0
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by Franck Tanoh (3 months ago)
Franck Tanoh (3 months ago)
Keyword search system against over 20 life sciences databases developed by DDBJ.
SOAP variant: http://www.biocatalogue.org/services/12
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
Base URL:
http://xml.nig.ac.jp/rest/Invoke?service=ARSA |
3 REST Endpoints
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90
0
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Annotations: 9
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9
0
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by Franck Tanoh (3 months ago)
Franck Tanoh (3 months ago)
Provides an easy way to retrieve entries from various databases at DDBJ.
SOAP variant: http://www.biocatalogue.org/services/10
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
Base URL:
http://xml.nig.ac.jp/rest/Invoke?service=GetEntry |
44 REST Endpoints
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80
0
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Annotations: 11
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11
0
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by Franck Tanoh (3 months ago)
Franck Tanoh (3 months ago)
Retrieve DDBJ entry
The DNA Data Bank of Japan (DDBJ) is one of three summit databanks that construct DDBJ/EMBL/GenBank International Nucleotide Sequence Database, through close collaboration with EBI in Europe and NCBI in USA.
SOAP variant: http://www.biocatalogue.org/services/9
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
Base URL:
http://xml.nig.ac.jp/rest/Invoke?service=DDBJ |
7 REST Endpoints
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Other Services Responsible For (0)
No entries found
Services Annotated (330)
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115
0
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This service has been archived because it may not be active anymore (or is close to being non active).
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74
0
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This service has been archived because it may not be active anymore (or is close to being non active).
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81
0
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This service has been archived because it may not be active anymore (or is close to being non active).
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90
0
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This service has been archived because it may not be active anymore (or is close to being non active).
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119
0
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Annotations: 80
14
19
47
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by Franck Tanoh (5 months ago)
Franck Tanoh (5 months ago)
Get OMIM (Online Mendelian Inheritance in Man) Information.
OMIM is a catalogue of a human genes and genetic disorders authored and edited by Dr. Victor A.McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information.
Website: http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
WSDL Location:
http://xml.nig.ac.jp/wsdl/OMIM.wsdl |
4 SOAP Operations
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999
 1
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Annotations: 217
42
69
106
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
BLAST finds regions of similarity between biological sequences.
This service might not be executable when servers for the analysis are busy. In this case, you will receive the following message:
'The search and analysis service is very busy now. Please try it again.'
by dave (4 months ago)
dave (4 months ago)
Uses the DDBJ's UniProt BLAST service that forms part of its Web API for Bioinformatics pages.
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
WSDL Location:
http://xml.nig.ac.jp/wsdl/Blast.wsdl |
8 SOAP Operations
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122
1
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Annotations: 30
3
15
12
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
The TFmodeller program scans a protein sequence P against a library of protein-DNA complexes and builds comparative models of P if good templates are found. These models are used to get an idea of the P-DNA interface, its evolution and the putative recognised DNA sequences.
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Provider:
University of Mexico (Center for Genomic Sciences of the National Autonomous)
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Submitter / Source:
WSDL Location:
http://maya.ccg.unam.mx:8080/axis/TFmodellerService.jws?WSDL |
1 SOAP Operation
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124
0
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Annotations: 16
0
16
0
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by Franck Tanoh (2 months ago)
Franck Tanoh (2 months ago)
Retrieves sequences in requested format from a list of one or more unique identifiers.
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Provider:
National Center for Biotechnology Information (NCBI)
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Submitter / Source:
WSDL Location:
http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_seq.wsdl |
1 SOAP Operation
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147
1
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Annotations: 99
23
76
0
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Retrieves information from the database of protein subcellular localization (DBSubLoc). This database contains proteins from primary protein database such as SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross referencs to taxonomies and Gene Ontology database.
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Provider:
Institute of Bioinformatics, Tsinghua University
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Submitter / Source:
WSDL Location:
http://www.bioinfo.tsinghua.edu.cn/~tigerchen/SubLoc.wsdl |
7 SOAP Operations
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113
0
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Annotations: 22
19
3
0
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from
provider's description doc
(2 months ago)
provider's description doc
(2 months ago)
Soap access to sequence databases at DKFZ
by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Allows you to retrieve entries from sequence databases at DKFZ (German Cancer Research Center)
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Provider:
German Cancer Research Center
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Submitter / Source:
WSDL Location:
http://genome.dkfz-heidelberg.de/menu/hobit/2005/04/SoapDB.wsdl |
5 SOAP Operations
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Favourites (8)
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726
2
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aka
WSDbfetch (RPC/encoded SOAP)
aka
WSDbfetch (SOAP)
aka
WSDbfetch
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Annotations: 126
28
98
0
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by Franck Tanoh (8 months ago)
Franck Tanoh (8 months ago)
The service retrieves entries (sequences, literature abstract, protein structure information, etc) from various up-to-date biological databases using databases entry identifiers or accession numbers.
Supported databases (complete list can be found on the web interface): EMBL, Ensembl, UniProt, UniRef, UniSave, RefSeq, Medline, PDB, InterPro, HGVbase, GenomeReviews, interPro.
Web interface: http://www.ebi.ac.uk/cgi-bin/dbfetch
by Hamish McWilliam (2 months ago)
Hamish McWilliam (2 months ago)
An equivalent document/literal SOAP interface to the service is also available (http://www.biocatalogue.org/services/2654).
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Provider:
European Bioinformatics Institute (EBI)
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Submitter / Source:
WSDL Location:
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl |
7 SOAP Operations
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291
1
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aka
WSInterProScan
aka
InterProScan
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Annotations: 72
29
41
2
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by joecker (8 months ago)
joecker (8 months ago)
InterProScan runs a lot of tools for protein domain prediction (against different databases). The results are mapped to InterPro identifiers to get additional information and identify same domains in different databases.
Please note that not all protein domains are included in InterPro, but are in the result of InterProScan.
by joecker (8 months ago)
joecker (8 months ago)
Please note that some tools in InterProScan use Hidden Markow Models and are therefore very slow.
by Franck Tanoh (8 months ago)
Franck Tanoh (8 months ago)
InterPro is a database of protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences. This service allows you to query your protein sequence or protein sequence identifier against InterPro.
Home: http://www.ebi.ac.uk/Tools/InterProScan/
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Provider:
European Bioinformatics Institute (EBI)
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Submitter / Source:
WSDL Location:
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl |
7 SOAP Operations
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265
1
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aka
EasyGene
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Annotations: 28
1
20
7
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from
provider's description doc
(about 1 year ago)
provider's description doc
(about 1 year ago)
The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic
DNA. Each prediction is attributed with a significance score (R-value) indicating how likely
it is to be just a non-coding open reading frame rather than a real gene. The user needs
only to specify the organism hosting the query sequence. Two more parameters (start codon
leniency and R-value cutoff) have default values which may be altered if needed.
http://www.cbs.dtu.dk/services/EasyGene/
This service is fully asynchronous; the usage is split into the following
three operations, which is usually executed in this order.
Procedures and messages used are either common and shared ...
by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Produces a list of predicted genes given a sequence of prokaryotic DNA.
Interface: http://www.cbs.dtu.dk/services/EasyGene/
by rapacki (4 months ago)
rapacki (4 months ago)
The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic
DNA. Each prediction is attributed with a significance score (R-value) indicating how likely
it is to be just a non-coding open reading frame rather than a real gene. The user needs
only to specify the organism hosting the query sequence. Two more parameters (start codon
leniency and R-value cutoff) have default values which may be altered if needed.
Alongside this Web Service EasyGene method is also implemented as an interactive server at: http://www.cbs.dtu.dk/services/EasyGene/
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Provider:
Center for Biological Sequence Analysis (CBS)
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Submitter / Source:
WSDL Location:
http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl |
3 SOAP Operations
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514
2
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Annotations: 1283
192
15
1076
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database of biological systems, consisting of genetic building blocks of genes and proteins (KEGG GENES), chemical building blocks of both endogenous and exogenous substances (KEGG LIGAND), molecular wiring diagrams of interaction and reaction networks (KEGG PATHWAY), and hierarchies and relationships of various biological objects (KEGG BRITE). KEGG provides a reference knowledge base for linking genomes to biological systems and also to environments by the processes of PATHWAY mapping and BRITE mapping.
This service allows you to access or retrieve data (genes, pathways, enzyme, drugs, etc) from KEGG.
KEGG home page: http://www.g...
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Provider:
KEGG
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Submitter / Source:
WSDL Location:
http://soap.genome.jp/KEGG.wsdl |
72 SOAP Operations
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165
1
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aka
PICR
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Annotations: 28
9
19
0
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by Rodrigo Lopez (about 1 year ago)
Rodrigo Lopez (about 1 year ago)
Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another.
The Protein Identifier Cross-Reference (PICR) service is a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references base...
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Provider:
European Bioinformatics Institute (EBI)
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Submitter / Source:
WSDL Location:
http://www.ebi.ac.uk/Tools/picr/service?wsdl |
3 SOAP Operations
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116
1
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aka
http://code.google.com/p/psicquic/wiki/RestAccess
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Annotations: 6
0
6
0
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by brunoaranda (8 months ago)
brunoaranda (8 months ago)
PSICQUIC is an effort from the HUPO Proteomics Standard Initiative (HUPO-PSI) to standardise the access to molecular interaction databases programmatically.
This specific implementation provides remote access to the MINT database.
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Provider:
Protemics Standard Initiative Common Query InterfaCe (PSICQUIC)
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Submitter / Source:
Base URL:
http://mint.bio.uniroma2.it/mint/psicquic/webservices/current/search/ |
0 REST Endpoints
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122
1
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Annotations: 30
3
15
12
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
The TFmodeller program scans a protein sequence P against a library of protein-DNA complexes and builds comparative models of P if good templates are found. These models are used to get an idea of the P-DNA interface, its evolution and the putative recognised DNA sequences.
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Provider:
University of Mexico (Center for Genomic Sciences of the National Autonomous)
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Submitter / Source:
WSDL Location:
http://maya.ccg.unam.mx:8080/axis/TFmodellerService.jws?WSDL |
1 SOAP Operation
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147
1
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Annotations: 99
23
76
0
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Retrieves information from the database of protein subcellular localization (DBSubLoc). This database contains proteins from primary protein database such as SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross referencs to taxonomies and Gene Ontology database.
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Provider:
Institute of Bioinformatics, Tsinghua University
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Submitter / Source:
WSDL Location:
http://www.bioinfo.tsinghua.edu.cn/~tigerchen/SubLoc.wsdl |
7 SOAP Operations
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