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Nucleic Acids Research Advance Access originally published online on October 11, 2007
Nucleic Acids Research 2008 36(Database issue):D524-D527; doi:10.1093/nar/gkm831
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Nucleic Acids Research, 2008, Vol. 36, Database issue D524-D527
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

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

Pere Puigbò*, Antoni Romeu and Santiago Garcia-Vallvé

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

* To whom correspondence should be addressed. Tel: +34 977558778; Fax: +34 977558232; Email: ppuigbo{at}urv.cat

Received July 24, 2007. Revised September 21, 2007. Accepted September 21, 2007.

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.


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