What's new
Jan 15 2010 ARSA database search (DDBJ, DAD) temporary unavailable
Oct 19 2009 Prokaryotic genomes annotation workflow was added in the workflow introduction page.
Sep 8 2009 Annotation workflow was added in the workflow introduction page.
Aug 6 2009 New API of high speed BLAST was added. Please refer to the page about high speed BLAST and API document.
Oct 19 2009 Prokaryotic genomes annotation workflow was added in the workflow introduction page.
Sep 8 2009 Annotation workflow was added in the workflow introduction page.
Aug 6 2009 New API of high speed BLAST was added. Please refer to the page about high speed BLAST and API document.
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 |
| Fasta | Finds regions of local similarity between Protein or DNA sequences developed by Virginia University. |
| VecScreen | A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin |
| 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. |
| GIBEnv | Genome Information Broker for Environmental samples (GIBEnv) is a database which is added annotation information against DDBJ environmental division. |
| 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 |
| RefSeq | The Reference Sequence (RefSeq) is developed by NCBI and provides a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms. |
| 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. |
| OMIM | Online Mendelian Inheritance in Man(OMIM) is a catalog of a human genes and genetic disorders developed by NCBI. |
| 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: Jan 15, 2010