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PMID: 22120661 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.

Database : the journal of biological databases and curation ·Vol. 2011 ·2011-00-00 ·Pages bar050

Di Génova A, Aravena A, Zapata L, González M, Maass A, Iturra P

Abstract

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/

MeSH Terms
Animals Computational Biology/methods Database Management Systems Databases, Genetic Internet Oncorhynchus mykiss/genetics Salmo salar/genetics User-Computer Interface
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Di Génova Alex
Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile.
Aravena Andrés
Zapata Luis
González Mauricio
Maass Alejandro
Iturra Patricia
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Article Info
Journal
Database : the journal of biological databases and curation
Abbr.
Database (Oxford)
ISSN
1758-0463
DOI
10.1093/database/bar050
Published
2011-00-00
Epub
2011-00-26
Pages
bar050
Language
English
Region
England
NLM ID
101517697
PMCID
PMC3225076
Subset
IM
External Links
PubMed source DOI: 10.1093/database/bar050 PMC Full Text View journal details
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