Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs) 英文参考文献.docVIP

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Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs) 英文参考文献.doc

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Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs) 英文参考文献

/2000/1/5/research/0009.1 Research Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs) Darren A Natale, Uma T Shankavaram, Michael Y Galperin, Yuri I Wolf, L Aravind and Eugene V Koonin Address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rockville Pike, Bethesda, MD 20894, USA. Correspondence: Eugene V Koonin. E-mail: koonin@ Published: 6 November 2000 Received: 19 June 2000 Revised: 25 August 2000 Accepted: 21 September 2000 GenomeBiology 2000, 1(5):research0009.1–0009.19 The electronic version of this article is the complete one and can be found online at /2000/1/5/research/0009 ? GenomeB (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi. Results: A. pernix and P. abyssi proteins were assigned to COGs using the COGNITOR program; the results were verified on a case-by-case basis and augmented by additional database searches using the PSI-BLAST and TBLASTN programs. Functions were predicted for over 300 proteins from A. pernix, which could not be assigned a function using conventional methods with a conservative sequence similarity threshold, an approximately 50% increase compared to the original annotation. A. pernix shares most of the conserved core of proteins that were previously identified in the Euryarchaeota. Cluster analysis or distance matrix tree construction based on the co-occurrence of genomes in COGs showed that A. pernix forms a distinct group within the arc