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Nucleic Acids Res. 2008 Jan;36(Database issue):D524-7. Epub 2007 Oct 11.

HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection.

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1
Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University (URV), c/Marcel-li Domingo, s/n. Campus Sescelades, 43007 Tarragona, Spain. ppuigbo@urv.cat

Abstract

The highly expressed genes database (HEG-DB) is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index (CAI) for all of the genes using the codon usage of the highly expressed genes as a reference set. The 'Pathway Tools Omics Viewer' from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes. The HEG-DB is freely available at http://genomes.urv.cat/HEG-DB.

PMID:
17933767
PMCID:
PMC2238906
DOI:
10.1093/nar/gkm831
[Indexed for MEDLINE]
Free PMC Article
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