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knotinframeImplementationService SOAP De
Views 30 Favourites 0
aka knotInframe
Annotations: 16 Total number of annotations from the provider's definition / description document. 5 Total number of annotations submitted by members of the BioCatalogue. 11 Total number of annotations sourced from other registries. 0
by Franck Tanoh (3 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.

Provider: Bielefeld University | Submitter / Source: Franck TanohGb (3 months ago)

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WSDL Location: http://bibiserv.techfak.uni-bielefeld.de/wsdl/knotinframe.wsdl | 2 SOAP Operations
PASSED
diArk - A resource for eukaryotic genome research REST De
Views 23 Favourites 0
Categories:
Annotations: 2 Total number of annotations from the provider's definition / description document. 0 Total number of annotations submitted by members of the BioCatalogue. 2 Total number of annotations sourced from other registries. 0
by mkollgr (3 months ago)
The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses yielded thousands of sequenced EST and cDNA clones. For the researcher interested in single gene analyses (from a phylogenetic, a structural biology or other perspective) it is therefore important to have up-to-date knowledge about the various resources providing primary data. diArk provides comprehensive search modules each with detailed options and three different views of the selected data.

Provider: diArk | Submitter / Source: mkollgrDe (3 months ago)

Tags on this service:
none
Base URL: http://www.diark.org | 0 REST Endpoints
PASSED
Find Similar BioModels REST De
Views 103 Favourites 0
Annotations: 12 Total number of annotations from the provider's definition / description document. 0 Total number of annotations submitted by members of the BioCatalogue. 12 Total number of annotations sourced from other registries. 0
by Falko Krause (6 months ago)
Model similarity search based on MIRIAM annotations. The result are BioModels similar the inserted BioModel id or the lists of lists of MIRIAM URNs. For further information please read our API documentation.

Provider: Semantic SBML | Submitter / Source: Falko KrauseDe (6 months ago)

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Base URL: http://www.semanticsbml.org/semanticSBML | 0 REST Endpoints
PASSED
Search MIRIAM annotations REST De
Views 84 Favourites 0
Annotations: 10 Total number of annotations from the provider's definition / description document. 0 Total number of annotations submitted by members of the BioCatalogue. 10 Total number of annotations sourced from other registries. 0
by Falko Krause (6 months ago)
Search for MIRIAM URNs that can be used for annotation. Return formats are human, json and xml. Please read our API documentation for more information.

Provider: Semantic SBML | Submitter / Source: Falko KrauseDe (6 months ago)

Tags on this service:
Base URL: http://www.semanticsbml.org/semanticSBML/annotate/search | 0 REST Endpoints
PASSED
STRING API REST De
Views 250 Favourites 0
aka string database aka string
Annotations: 6 Total number of annotations from the provider's definition / description document. 0 Total number of annotations submitted by members of the BioCatalogue. 6 Total number of annotations sourced from other registries. 0
by Alex (about 1 year ago)
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. STRING home page: http://string-db.org/

Provider: STRING | Submitter / Source: AlexCh (about 1 year ago)

Tags on this service:
none
Base URL: http://string-db.org/api/ | 0 REST Endpoints
WARNING
SMART SOAP De
Views 71 Favourites 0
Categories:
Annotations: 15 Total number of annotations from the provider's definition / description document. 4 Total number of annotations submitted by members of the BioCatalogue. 9 Total number of annotations sourced from other registries. 2
from provider's description doc (3 months ago)
SMART webservice
by iletunic (6 months ago)
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 700 domain families found in signaling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. The webservice accepts either a protein sequence or Uniprot/Ensembl protein identifiers. If both a sequence and an ID are supplied, ID will be used. Only sequences that are present in the SMART database will be accepted (Uniref100 and Ensembl proteomes).

Provider: EMBL Nucleotide Sequence Database (Hiedelberg) | Submitter / Source: iletunic (about 1 year ago)

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WSDL Location: http://smart.embl.de/webservice/SMART_webservice.wsdl | 1 SOAP Operation
PASSED
The ELM Resource Conservation Filter SOAP De
Views 73 Favourites 0
Categories:
Annotations: 26 Total number of annotations from the provider's definition / description document. 13 Total number of annotations submitted by members of the BioCatalogue. 10 Total number of annotations sourced from other registries. 3
from provider's description doc (3 months ago)
This WSDL file describe the Conservation Score Web Service. It calculates the conservation of ELM matches in a set of homologous sequences. A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. Claudia Chica, Alberto Labarga, Cathryn M Gould, Rodrigo Lopez and Toby J Gibson. BMC Bioinformatics. 2008 May 6; 9(1):229. http://conscore.embl.de/webservice/clients/conScorer.txt The CS Web Service should also be accessible via a graphical interface using the Cinema software. Cinema is a tool for annotated multiple alignmen...
by kate (6 months ago)
This service calculates the conservation of ELM matches in a set of homologous sequences. the web service consists of three methods: RunJob GetStatus GetResult Reference: A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. Claudia Chica, Alberto Labarga, Cathryn M Gould, Rodrigo Lopez and Toby J Gibson. BMC Bioinformatics. 2008 May 6;9(1):229

Provider: EMBL Nucleotide Sequence Database (Hiedelberg) | Submitter / Source: kate (about 1 year ago)

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WSDL Location: http://conscore.embl.de/webservice/CS.wsdl | 3 SOAP Operations
PASSED
GlobPlot SOAP De
Views 73 Favourites 0
Categories:
Annotations: 16 Total number of annotations from the provider's definition / description document. 5 Total number of annotations submitted by members of the BioCatalogue. 8 Total number of annotations sourced from other registries. 3
from provider's description doc (3 months ago)
This WSDL file describe the GlobPlot Web Service. It performs intrinsic protein disorder, domain and globularity prediction. GlobPlot: Exploring Protein Sequences for Globularity and Disorder Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson (Nucleic Acids Research, 2003, Vol. 31, No. 13 3701-3708) http://globplot.embl.de http://globplot.embl.de/clients/globPlotClient.txt
by kate (6 months ago)
GlobPlot performs intrinsic protein disorder, domain and globularity prediction for a query protein sequence. the web service consists of one method: runGlobPlotter Reference: GlobPlot: Exploring Protein Sequences for Globularity and Disorder Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson (Nucleic Acids Research, 2003, Vol. 31, No. 13 3701-3708) URL: globplot

Provider: EMBL Nucleotide Sequence Database (Hiedelberg) | Submitter / Source: kate (about 1 year ago)

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WSDL Location: http://globplot.embl.de/webservice/globplot.wsdl | 1 SOAP Operation
PASSED
The ELM Resource Structure Filter SOAP De
Views 58 Favourites 0
Annotations: 26 Total number of annotations from the provider's definition / description document. 13 Total number of annotations submitted by members of the BioCatalogue. 10 Total number of annotations sourced from other registries. 3
from provider's description doc (3 months ago)
This WSDL file describe the Structure Filter Web Service. This web service is useful for evaluating the location of candidate short regulatory sequences in proteins (linear motifs) which need to be accessible to interact with their ligand domains. The StructureFilter web-service calculates an accessibility score, secondary structure score and total score (as well as various other features) for each match of a regular expression or ELM in the query sequence for which structural information is available. (If a regular expression match is determined as having no associated structural information available, no reference is made to this match in the result set.) ...
by kate (6 months ago)
This web service is useful for evaluating the location of candidate short regulatory sequences in proteins (linear motifs) which need to be accessible to interact with their ligand domains. The StructureFilter web-service calculates an accessibility score, secondary structure score and total score (as well as various other features) for each match of a regular expression or ELM in the query sequence for which structural information is available. (If a regular expression match is determined as having no associated structural information available, no reference is made to this match in the result set.) the web service consists of three methods: RunJob GetStatus GetResult Referen...

Provider: EMBL Nucleotide Sequence Database (Hiedelberg) | Submitter / Source: kate (about 1 year ago)

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WSDL Location: http://structurefilter.embl.de/webservice/structureFilter.wsdl | 3 SOAP Operations
PASSED
SMART SOAP De
Views 56 Favourites 0
Categories:
Annotations: 15 Total number of annotations from the provider's definition / description document. 4 Total number of annotations submitted by members of the BioCatalogue. 9 Total number of annotations sourced from other registries. 2
from provider's description doc (3 months ago)
SMART webservice
by steve.pettifer (6 months ago)
SMART can predict possible catalytic inactivity, based on the presence of essential amino acids at specific positions in the alignment. If any of the required amino acids are missing, the domain is marked as 'inactive'.

Provider: EMBL Nucleotide Sequence Database (Hiedelberg) | Submitter / Source: steve.pettiferGb (about 1 year ago)

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WSDL Location: http://smart.embl-heidelberg.de/webservice/SMART_webservice.wsdl | 1 SOAP Operation
PASSED