Database

Extension of the COG and arCOG databases by amino acid and nucleotide sequences

Florian Meereis and Michael Kaufmann

The Protein Chemistry Group, Witten/Herdecke University, Stockumer Str. 10, 58448 Witten, Germany

author email corresponding author email

BMC Bioinformatics 2008, 9:479doi:10.1186/1471-2105-9-479

Published:	13 November 2008

Abstract

Background

The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequences corresponding to their protein or protein domain entries.

Results

Using sequence information obtained from GenBank flat files covering the completely sequenced genomes of the COG and arCOG databases, we constructed NUCOCOG (nucleotide sequences containing COG databases) as an extended version including all nucleotide sequences and in addition the amino acid sequences originally utilized to construct the current COG and arCOG databases. We make available three comprehensive single XML files containing the complete databases including all sequence information. In addition, we provide a web interface as a utility suitable to browse the NUCOCOG database for sequence retrieval. The database is accessible at http://www.uni-wh.de/nucocog webcite.

Conclusion

NUCOCOG offers the possibility to analyze any sequence related property in the context of the COG and arCOG framework simply by using script languages such as PERL applied to a large but single XML document.