Franck Tanoh (about 1 year ago)
HOGENOM (Database of Complete Genome Homologous Genes Families) home page: http://pbil.univ-lyon1.fr/databases/hogenom.php
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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 31
 0
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Annotations: 14
 8
6
 0
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago) |
Provider:
PRABI - Rhone-Alpes Bioinformatics Center
|
Submitter / Source:
WSDL Location:
http://prodom.prabi.fr/prodom/current/wsdl/hogenom.wsdl |
2 SOAP Operations
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 |
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53
0
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aka
psi-blast prodom database
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Annotations: 23
13
10
0
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Performs a recursive psi-blast against the ProDom database.
ProDom database website: http://prodom.prabi.fr/prodom/current/html/home.php
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Provider:
PRABI - Rhone-Alpes Bioinformatics Center
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Submitter / Source:
WSDL Location:
http://prodom.prabi.fr/prodom/current/wsdl/blastprodom.wsdl |
2 SOAP Operations
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109
0
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aka
blast prodom database
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Annotations: 28
2
23
3
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from
provider's description doc
(about 1 year ago)
provider's description doc
(about 1 year ago)
Contact : Daniel Kahn, kahn@biomserv.univ-lyon1.fr
Reference : Servant F, Bru C, Carrière S, Courcelle E, Gouzy J, Peyruc D, Kahn D (2002) ProDom: Automated clustering of homologous domains. Briefings in Bioinformatics. vol 3, no 3:246-251
by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Executes blast on a blast (blastn or blastp) on ProDom database (protein domain database).
ProDom database home page: http://prodom.prabi.fr/prodom/current/html/home.php
by lauranne.duquenne (6 months ago)
lauranne.duquenne (6 months ago)
blastProDom performs a blast (blastx or blastp) on the protein domain family database ProDom : enter a sequence (nucleotides or proteins, raw or fasta format) and it returns a blast output with the name of the families corresponding to the hits found, and a URL to get the image visualizing the blasted domains on the protein.
A perl script is available to run this webservice from your computer. Please install SOAP Lite before.
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Provider:
PRABI - Rhone-Alpes Bioinformatics Center
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Submitter / Source:
WSDL Location:
http://prodom.prabi.fr/prodom/current/wsdl/blastliteral.wsdl |
1 SOAP Operation
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30
0
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aka
Plant Transcription Factor Databases
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Annotations: 34
14
20
0
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Allow access and retrieval of information from the Plant Transcription Factor Databases
Home page: http://planttfdb.cbi.pku.edu.cn/
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Provider:
Peking University
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Submitter / Source:
WSDL Location:
http://planttfdb.cbi.pku.edu.cn/webservice/server.php?wsdl |
6 SOAP Operations
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38
0
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Annotations: 58
49
5
4
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Web service interface for the Mouse atlas project. The service is used to retrieve information from the EMAP database.
Home page: http://genex.hgu.mrc.ac.uk/
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Provider:
eMAP
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Submitter / Source:
WSDL Location:
http://genex.hgu.mrc.ac.uk/axis/services/ma?wsdl |
17 SOAP Operations
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77
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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38
0
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aka
Regulatory Sequence Analysis Tools (RSAT)
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Annotations: 50
46
4
0
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
Web services for the Regulatory Sequence Analysis Tools (RSAT). Tools developed by Jacques van Helden (jvanheld@bigre.ulb.ac.be), SOAP/WSDL interface developed by Olivier Sand (oly@bigre.ulb.ac.be).
by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Provides a series of operations designed for the detection of regulatory signals in non-coding sequences.
Home page: http://rsat.ccb.sickkids.ca/RSAT_home.cgi
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Provider:
Regulatory Sequence Analysis Tools (RSAT)
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Submitter / Source:
WSDL Location:
http://rsat.ccb.sickkids.ca/web_services/RSATWS.wsdl |
45 SOAP Operations
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23
0
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aka
getCabriBacteriaEntriesByIds
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Annotations: 62
62
0
0
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No description(s) yet
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Provider:
National Cancer Research Institute of Genoa, Italy (NCRI)
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Submitter / Source:
Soaplab Server Base URL:
http://bioinformatics.istge.it:8080/axis/services |
WSDL Location:
http://bioinformatics.istge.it:8080/axis/services/cabri_getz_services.getCabriBacteriaEntriesByIds?wsdl |
23 SOAP Operations
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33
0
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Annotations: 62
62
0
0
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No description(s) yet
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Provider:
National Cancer Research Institute of Genoa, Italy (NCRI)
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Submitter / Source:
Soaplab Server Base URL:
http://bioinformatics.istge.it:8080/axis/services |
WSDL Location:
http://bioinformatics.istge.it:8080/axis/services/cabri_getz_services.getCabriCellLinesEntriesByIds?wsdl |
23 SOAP Operations
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20
0
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aka
getCabriIdsByField
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Annotations: 62
62
0
0
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No description(s) yet
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Provider:
National Cancer Research Institute of Genoa, Italy (NCRI)
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Submitter / Source:
Soaplab Server Base URL:
http://bioinformatics.istge.it:8080/axis/services |
WSDL Location:
http://bioinformatics.istge.it:8080/axis/services/cabri_getz_services.getCabriIdsByField?wsdl |
23 SOAP Operations
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Other Services Responsible For (0)
No entries found
Services Annotated (333)
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111
0
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aka
BLASTatlas
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Annotations: 26
1
16
9
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from
provider's description doc
(about 1 year ago)
provider's description doc
(about 1 year ago)
This service creates maps of genome homology of a list of sequences against a reference
genome using either blastp, blastn, tblastn, or blastx.
The resolution is per-residue or per nucleotide depending on the regime of the blast
search: For each annotation in the reference genome, the best hit in the database
genome is found using one of the above algorithms. Each matching or mismatching
residue/nucleotide of the best hit (based on BLAST score) is then mapped back to the
genome sequence, using the coordinates provided in the annotations.
In the following, 'database' refers to the sequences being searched whereas
'reference' refers to the genome ...
by pfhallin (6 months ago)
pfhallin (6 months ago)
This BLASTatlas service creates maps of genome homology of a list of sequences against a reference
genome using either blastp, blastn, tblastn, or blastx.
The resolution is per-residue or per nucleotide depending on the regime of the blast
search: For each annotation in the reference genome, the best hit in the database
genome is found using one of the above algorithms. Each matching or mismatching
residue/nucleotide of the best hit (based on BLAST score) is then mapped back to the
genome sequence, using the coordinates provided in the annotations.
In the following, 'database' refers to the sequences being searched whereas
'reference' refers to the genome on to which the search is map...
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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/BLASTatlas/BLASTatlas_1_0_ws2.wsdl |
3 SOAP Operations
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 |
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60
0
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Annotations: 16
1
11
4
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from
provider's description doc
(about 1 year ago)
provider's description doc
(about 1 year ago)
SIDDbase-WS is a SOAP based Web Service created in a collaboration between the
Comparative Microbial Genomics Group at CBS, The Technical University of Denmark and
Prof. Craig Benham's research group at the UC Davis Genome Center. It provides
interoperable access to the SIDD software, and access to the repository of stored
results from calculations previously performed on complete bacterial genomes.
SIDD (Stress-induced DNA Duplex Destabilization) is the propensity for the DNA duplex to
be destabilized within genomic regions that are experiencing a superhelical stress. This
is a complex, interactive attribute of genomic DNA, that has been implicated in a wide
variety...
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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/SIDDbase/SIDDbase_1_0.wsdl |
4 SOAP Operations
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324
 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 (6 months ago)
rapacki (6 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/
|
Provider:
Center for Biological Sequence Analysis (CBS)
|
Submitter / Source:
WSDL Location:
http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl |
3 SOAP Operations
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63
0
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aka
NetChop - Prediction of proteasomal cleavages (MHC ligands)
aka
NetChop
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Annotations: 19
1
10
8
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from
provider's description doc
(about 1 year ago)
provider's description doc
(about 1 year ago)
INTRODUCTION
This Web Service implements NetChop v. 3.1. It produces neural network
predictions for cleavage sites of the human proteasome. The method is
described in detail in the following article:
The role of the proteasome in generating cytotoxic T cell epitopes:
Insights obtained from improved predictions of proteasomal cleavage.
M Nielsen, C Lundegaard, O Lund, and C Kesmir.
Immunogenetics., 57(1-2):33-41, 2005.
Alongside this Web Service the NetChop method is also implemented as
a traditional click-and-paste WWW server at:
http://www.cbs.dtu.dk/services/NetChop/
NetChop is also available as a stand-alone software package to install
and ...
by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Predict cleavage sites of the human proteasome.
interface: http://www.cbs.dtu.dk/services/NetChop/
by The EMBRACE Registry (about 1 year ago)
The EMBRACE Registry (about 1 year ago)
NetChop produces neural network
predictions for cleavage sites of the human proteasome. The method is
described in detail in the following article:
The role of the proteasome in generating cytotoxic T cell epitopes:
Insights obtained from improved predictions of proteasomal cleavage.
M Nielsen, C Lundegaard, O Lund, and C Kesmir.
Immunogenetics., 57(1-2):33-41, 2005.
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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/NetChop/NetChop_3_1.wsdl |
3 SOAP Operations
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176
0
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aka
BIND
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Annotations: 162
39
6
117
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by Franck Tanoh (4 months ago)
Franck Tanoh (4 months ago)
Allow access to BIND (Biomolecular Interaction Network Database) interaction, molecular complex, and pathway data. Note that the BIND database is no more public: http://www.nature.com/nbt/journal/v24/n2/full/nbt0206-115.html
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Provider:
Thomsom Reuters
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Submitter / Source:
WSDL Location:
http://soap.bind.ca/wsdl/bind.wsdl |
12 SOAP Operations
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98
0
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Annotations: 35
25
8
2
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by Franck Tanoh (2 months ago)
Franck Tanoh (2 months ago)
GeneCruiser allows users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers from databases, such as UniGene, while providing links to web resources, such as the UCSC Genome Browser.
website: http://genecruiser.broadinstitute.org/genecruiser3/pages/index.jsf
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Provider:
GenePattern
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Submitter / Source:
WSDL Location:
http://www.broad.mit.edu/webservices/genecruiser/services/Annotation?wsdl |
10 SOAP Operations
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83
0
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Annotations: 330
321
4
5
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by Franck Tanoh (2 months ago)
Franck Tanoh (2 months ago)
Allows access and the retrieval of information from the e-Fungi warehouse, an integrated data from multiple fungal genomes.
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Provider:
e-Fungi
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Submitter / Source:
WSDL Location:
http://beaconw.cs.manchester.ac.uk/axis/services/efungi?wsdl |
92 SOAP Operations
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97
0
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Annotations: 27
7
20
0
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Term management system.
Web Interface: http://www.nactem.ac.uk/software/termine/
by George Moulton (9 months ago)
George Moulton (9 months ago)
Input some source text and retrieve a list of terms discovered, ranked by their importance within the text.
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Provider:
Nactem
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Submitter / Source:
WSDL Location:
http://www.nactem.ac.uk/software/termine/webservice/termine.wsdl |
1 SOAP Operation
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37
0
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Annotations: 11
5
4
2
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
This service performs the basic mapping of ELM motifs to a query sequence. The service returns all matching ELMs to a query sequence. Note that this is not a complete prediction of functional site. Extensive filtering of the resulting list of ELMs will be necessary.
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll, P., Linding, R., Gemnd, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D. M. A., Ausiello, G., Brannetti, B., Costantini, A.,
Ferr, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, L., Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P.,
Rychlewski,...
by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
This service performs the basic mapping of ELM (Eucaryotic Linear Motifs) motifs to a query sequence. The service returns all matching ELMs to a query sequence. Note that this is not a complete prediction of functional site. Extensive filtering of the resulting list of ELMs will be necessary.
Web site: http://elm.eu.org/
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Provider:
Bergen Center for Computational Science
|
Submitter / Source:
WSDL Location:
http://api.bioinfo.no/wsdl/ELMMatcher.wsdl |
1 SOAP Operation
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52
0
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Annotations: 27
21
4
2
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
This WSDL file describe the ELM Instance Mapper Web Service. It compares a query protein sequence with sequences known to contain ELM Instances.
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll, P., Linding, R., Gemnd, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D. M. A., Ausiello, G., Brannetti, B., Costantini, A.,
Ferr, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, L., Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P.,
Rychlewski, L., Kster, B., Helmer-Citterich, M., Hunter, W. N., Aasland, R., Gibson, T. J. (2003). Nucleic Acids Res., 31: 3625-3630...
by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
The ELM instance mapper uses PHI-BLAST to map ELM predictions of a query sequence to known annotated ELM instances. The basis for the mapping is sequence similarity and positional conservation of the motif. If an ELM prediction is mapped to a known ELM instance, the prediction is given a score from 0 to 1, where 1 means that the query sequence is identical to the database sequence, and the prediction can be considered an experimentally verified ELM instance.
The result of a successful ELM instance mapping is the raw PHI-BLAST output and a summary of the results with the calculated score.
website: http://elm.eu.org/
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Provider:
Bergen Center for Computational Science
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Submitter / Source:
WSDL Location:
http://api.bioinfo.no/wsdl/ELMInstanceMapper.wsdl |
5 SOAP Operations
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Favourites (8)
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796
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 (9 months ago)
Franck Tanoh (9 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 (3 months ago)
Hamish McWilliam (3 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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309
1
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aka
WSInterProScan
aka
InterProScan
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Annotations: 72
29
41
2
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by joecker (9 months ago)
joecker (9 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 (9 months ago)
joecker (9 months ago)
Please note that some tools in InterProScan use Hidden Markow Models and are therefore very slow.
by Franck Tanoh (9 months ago)
Franck Tanoh (9 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)
|
Submitter / Source:
WSDL Location:
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl |
7 SOAP Operations
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324
1
|
|
aka
EasyGene
|
Annotations: 28
1
20
7
|
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 (6 months ago)
rapacki (6 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/
|
Provider:
Center for Biological Sequence Analysis (CBS)
|
Submitter / Source:
WSDL Location:
http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl |
3 SOAP Operations
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548
2
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|
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Annotations: 1283
192
15
1076
|
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
|
Submitter / Source:
WSDL Location:
http://soap.genome.jp/KEGG.wsdl |
72 SOAP Operations
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184
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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123
1
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|
aka
http://code.google.com/p/psicquic/wiki/RestAccess
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Annotations: 6
0
6
0
|
by brunoaranda (10 months ago)
brunoaranda (10 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)
|
Submitter / Source:
Base URL:
http://mint.bio.uniroma2.it/mint/psicquic/webservices/current/search/version |
0 REST Endpoints
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|
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128
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)
|
Submitter / Source:
WSDL Location:
http://maya.ccg.unam.mx:8080/axis/TFmodellerService.jws?WSDL |
1 SOAP Operation
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154
1
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|
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Annotations: 99
23
76
0
|
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
|
Submitter / Source:
WSDL Location:
http://www.bioinfo.tsinghua.edu.cn/~tigerchen/SubLoc.wsdl |
7 SOAP Operations
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