What's new
May 21 2010 GIBEnv service will be will be terminated on May 25 2010.
May 21 2010 getXMLEntry service and getFeatureInfo service in DDBJ service, getXML_DDBJEntry service in GetEntry service will be terminated on May 25 2010.
May 07 2010 Workflow Navigation System was upgraded.
May 21 2010 getXMLEntry service and getFeatureInfo service in DDBJ service, getXML_DDBJEntry service in GetEntry service will be terminated on May 25 2010.
May 07 2010 Workflow Navigation System was upgraded.
Bioinformatics web service
Web services in the world
Available services
| Data retrieve and keyword search | |
| Service name | Overview |
|---|---|
| DDBJ | Retrieve DDBJ entry |
| GetEntry | Database search and entry retrieve by accession number against DDBJ and other biological molecular database. |
| ARSA | Keyword search system against over 20 life sciences databases developed by DDBJ |
| Sequence search and analysis | |
| Service name | Overview |
| Blast | Finds regions of similarity between biological sequences developed by NCBI |
| ClustalW | Multiple sequence alignment program for DNA or proteins developed by EBI |
| Mafft | Multiple alignment program for amino acid or nucleotide sequeces developed in Kyoto Univ and Kyushu Univ |
| VecScreen | A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin |
| PhylogeneticTree | Generate phylogenetic from phylip format data. |
| DDBJ original system | |
| Service name | Overview |
| Gib | Genome Information Broker (GIB) is the comprehensive data repository of complete microbial genomes in the public domain. |
| Gtop | Genome To Protein (GTOP) is a database which summarizes analysis results against coding sequences identified by various genome projects. |
| GTPS | Gene Trek in Prokaryote Space (GTPS) is a database which is re-annotated ORFs against microorganism genome data in DDBJ database. |
| GIBV | Genome Information Broker for Viruses (GIB-V) is a complete virus genome data repository extracted from DDBJ database. |
| GIBIS | Genome Information Broker for Insertion Sequence (GIBIS) is a database containing whole bacterial IS data obtained by extracting IS region from publicized nucleotide sequences of DDBJ. |
| SPS | Splicing Profile based Score (SPS) is a new method to compare two amino acid sequences. |
| Other public database system | |
| Service name | Overview |
| TxSearch | A retrieval system for Taxonomy Database which was unified by DDBJ, GenBank and EMBL |
| Ensembl | Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. |
| NCBIGenomeAnnotation | NCBI Genome annotation is a summary of NCBI genome database. |
| GO | The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. |
| Getting result which is called asynchronously | |
| Service name | Overview |
| RequestManager | A service for getting result which is called asynchronously |
Workflow Navigation System
You can use several bioinformatics service with common web interface. This system provides not only the result of service but also the next services.
Links for bioinformatics[Reference] Yeondae Kwon, Yasumasa Shigemoto, Yoshikazu Kuwana and Hideaki Sugawara "Web API for biology with a workflow navigation system" Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W11-W16
[Reference] Sugawara H, Miyazaki S. Biological SOAP servers and web services provided by the public sequence data bank. Nucleic Acids Res. 2003 Jul 1;31(13):3836-9
"Web API for Biology" was supported in 2003-2005 by the project of "Research and Development of Biological Portal Site of the New Generation" and continues developing in the BIRD project.
Last Updated: Jun 25, 2010