Franck Tanoh (3 months ago)
The REPuter program family provides state of the art software solutions to compute and visualize repeats in whole genomes or chromosomes.
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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 63
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reputer
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Annotations: 26
 16
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by Franck Tanoh (3 months ago)
Franck Tanoh (3 months ago) |
Provider:
Bielefeld University
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Submitter / Source:
WSDL Location:
http://bibiserv.techfak.uni-bielefeld.de/wsdl/REPuter.wsdl |
4 SOAP Operations
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25
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dialign
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Annotations: 27
23
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
DIALIGN is a multiple sequence alignment program. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies.
Paper published: http://www.almob.org/content/3/1/6/abstract/
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Provider:
Bielefeld University
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Submitter / Source:
WSDL Location:
http://bibiserv.techfak.uni-bielefeld.de/wsdl/dialign.wsdl |
7 SOAP Operations
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73
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pknot
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Annotations: 42
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
pknotsRG is a tool for folding RNA secondary structures, including the class of simple recursive pseudoknots. It is limited to sequences of length up to 800 bases.
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Provider:
Bielefeld University
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Submitter / Source:
WSDL Location:
http://bibiserv.techfak.uni-bielefeld.de/wsdl/pknotsRG.wsdl |
5 SOAP Operations
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52
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RNAfold
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Annotations: 23
15
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4
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Webservice interface for RNA folding and sequence design using the program RNAfold from the Vienna package ( http://www.tbi.univie.ac.at/~ivo/RNA/ ). Currently RNAfold from Vienna package version 1.4.
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Provider:
Bielefeld University
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Submitter / Source:
WSDL Location:
http://bibiserv.techfak.uni-bielefeld.de/wsdl/RNAfold.wsdl |
5 SOAP Operations
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121
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SignalP - Prediction of signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
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Annotations: 25
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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 SignalP v. 3.1. It predicts the presence and
location of signal peptide cleavage sites in amino acid sequences from
different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes,
and eukaryotes. The method incorporates a prediction of cleavage sites
and a signal peptide/non-signal peptide prediction based on a combination
of several artificial neural networks and hidden Markov models. The method
is described in detail in the following article:
Improved prediction of signal peptides: SignalP 3.0.
J D Bendtsen, H Nielsen, G v Heijne and S Brunak.
J. Mol. Biol., 340:783-795, 2004.
The difference between v. 3.0 a...
by rapacki (6 months ago)
rapacki (6 months ago)
This Web Service implements SignalP v. 3.1. It predicts the presence and
location of signal peptide cleavage sites in amino acid sequences from
different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes,
and eukaryotes. The method incorporates a prediction of cleavage sites
and a signal peptide/non-signal peptide prediction based on a combination
of several artificial neural networks and hidden Markov models. The method
is described in detail in the following article:
Improved prediction of signal peptides: SignalP 3.0.
J D Bendtsen, H Nielsen, G v Heijne and S Brunak.
J. Mol. Biol., 340:783-795, 2004.
Alongside this Web Service the SignalP method is also imp...
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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/SignalP/SignalP_3_1_ws0.wsdl |
3 SOAP Operations
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47
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RNAshapes
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Annotations: 27
17
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
RNAshapes offers three powerful RNA analysis tools
* Computation of a small set of representative structures of different shapes, complete in a well-defined sense.
* Computation of accumulated shape probabilities.
* Comparative prediction of consensus structures, as an alternative to the over-expensive Sankoff Algorithm.
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Provider:
Bielefeld University
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Submitter / Source:
WSDL Location:
http://bibiserv.techfak.uni-bielefeld.de/wsdl/RNAshapes.wsdl |
5 SOAP Operations
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23
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Annotations: 28
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by Franck Tanoh (2 months ago)
Franck Tanoh (2 months ago)
Allows access to the PRODORIC database. This includes the search for regulons, DNA binding sites and expression data. PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.
website: http://prodoric.tu-bs.de/
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Provider:
PRODORIC
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Submitter / Source:
WSDL Location:
http://134.169.104.13/webservice/prodoric.wsdl |
8 SOAP Operations
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33
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EST_to_GenomicSequence
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Annotations: 16
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
E2G efficiently maps large EST and cDNA data sets to genomic DNA. The server hosts huge EST databases of a few GB in size in indexed data structure. This allows users to
-rapidly detect new genes
-verify the exon-intron structure of predicted genes
-determine splice variants
in the uploaded genomic region of interest.
The Web interface provides a graphical view of the results. Alignments can be visualized and matching sequences downloaded for further processing.
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Provider:
Bielefeld University
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Submitter / Source:
WSDL Location:
http://bibiserv.techfak.uni-bielefeld.de/wsdl/e2g.wsdl |
3 SOAP Operations
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123
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Annotations: 22
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from
provider's description doc
(3 months ago)
provider's description doc
(3 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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154
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Annotations: 99
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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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Other Services Responsible For (0)
No entries found
Services Annotated (333)
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178
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Annotations: 13
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13
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
This service allows you to access and retrieve data from the pfam database. The Pfam database is a large collection of protein domain families. Each family is represented by multiple sequence alignments and hidden Markov models (HMMs).
To return the accession and ID for a Pfam family, given either the ID or accession as input. Any of the following URLs will return the same simple XML document:
http://pfam.sanger.ac.uk/family/acc?id=Piwi&output=xml
http://pfam.sanger.ac.uk/family/acc/Piwi?output=xml
http://pfam.sanger.ac.uk/family/id?output=xml&acc=PF02171
http://pfam.sanger.ac.uk/family/id/Piwi?output=xml
http://pfam.sanger.ac.uk/family?entry=Piwi&output=xml
You can retrieve ...
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Provider:
Sanger Institute
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Submitter / Source:
Base URL:
http://pfam.sanger.ac.uk/ |
0 REST Endpoints
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93
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Maxsprout
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Annotations: 51
31
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
MaxSprout is a database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimised in rotamer space using a rough potential energy function to avoid clashes.
web interface: http://www.ebi.ac.uk/Tools/maxsprout/
by Hamish McWilliam (6 months ago)
Hamish McWilliam (6 months ago)
Generate protein backbone and side chain co-ordinates from a C(alpha) trace in PDB format using the MaxSprout program.
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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/WSMaxsprout.wsdl |
7 SOAP Operations
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128
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arrayexpress
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Annotations: 8
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by Rodrigo Lopez (about 1 year ago)
Rodrigo Lopez (about 1 year ago)
Data in the ArrayExpress Archive, Warehouse and Atlas of gene expression can be programmatically accessed via REST and SOAP interfaces.
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Provider:
European Bioinformatics Institute (EBI)
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Submitter / Source:
Base URL:
http://www.ebi.ac.uk/microarray-as/ae/xml/experiments/ |
0 REST Endpoints
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152
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WSDbfetch (REST)
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dbfetch
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Annotations: 21
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21
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by Rodrigo Lopez (about 1 year ago)
Rodrigo Lopez (about 1 year ago)
WSDbfetch allows you to retrieve entries from various up-to-date biological databases using entry identifiers or accession numbers. This is equivalent to the CGI based dbfetch service. Like the CGI service a request can return a maximum of 200 entries.
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Provider:
European Bioinformatics Institute (EBI)
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Submitter / Source:
Base URL:
http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch |
0 REST Endpoints
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46
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Annotations: 6
3
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
Authority: llama.med.harvard.edu - Protein-protein interactions using spoke model (direct bait-prey
interactions only), by Gavin et al.
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Provider:
Harvard Medical School
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Submitter / Source:
WSDL Location:
http://biomoby.org/services/wsdl/llama.med.harvard.edu/GavinSpoke |
1 SOAP Operation
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58
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Annotations: 6
3
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
Authority: llama.med.harvard.edu - Protein-protein interactions supported by a least one co-occurrence in
literature, as included in work of Rual et al. (2005).
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Provider:
Harvard Medical School
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Submitter / Source:
WSDL Location:
http://biomoby.org/services/wsdl/llama.med.harvard.edu/LCI |
1 SOAP Operation
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71
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Annotations: 7
3
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2
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
Authority: llama.med.harvard.edu - Pairs of genes whose expression profiles are correlated at a
significance level of p=0.05 or better.
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Provider:
Harvard Medical School
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Submitter / Source:
WSDL Location:
http://biomoby.org/services/wsdl/llama.med.harvard.edu/Su |
1 SOAP Operation
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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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76
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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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72
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This service has been archived because it may not be active anymore (or is close to being non active).
Favourites (8)
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796
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WSDbfetch (RPC/encoded SOAP)
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WSDbfetch (SOAP)
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WSDbfetch
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Annotations: 126
28
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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
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WSInterProScan
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InterProScan
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Annotations: 72
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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)
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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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324
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EasyGene
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Annotations: 28
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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/
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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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548
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Annotations: 1283
192
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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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184
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PICR
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Annotations: 28
9
19
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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
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aka
http://code.google.com/p/psicquic/wiki/RestAccess
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Annotations: 6
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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)
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Submitter / Source:
Base URL:
http://mint.bio.uniroma2.it/mint/psicquic/webservices/current/search/version |
0 REST Endpoints
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128
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Annotations: 30
3
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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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154
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Annotations: 99
23
76
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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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