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Bioinformatics Advance Access originally published online on February 5, 2004
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Bioinformatics 20(7) © Oxford University Press 2004; all rights reserved.

Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus

Ramakant Sharma {dagger}, Jitendra Kumar Maheshwari {dagger}, Tulika Prakash , Debasis Dash and Samir K. Brahmachari *

Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India

Received on July 28, 2003; revised on September 18, 2003; accepted on November 7, 2003
Advance Access Publication February 5, 2004

Motivation: The recent outbreak of severe acute respiratory syndrome (SARS) caused by SARS coronavirus (SARS-CoV) has necessitated an in-depth molecular understanding of the virus to identify new drug targets. The availability of complete genome sequence of several strains of SARS virus provides the possibility of identification of protein-coding genes and defining their functions. Computational approach to identify protein-coding genes and their putative functions will help in designing experimental protocols.

Results: In this paper, a novel analysis of SARS genome using gene prediction method GeneDecipher developed in our laboratory has been presented. Each of the 18 newly sequenced SARS-CoV genomes has been analyzed using GeneDecipher. In addition to polyprotein 1ab1, polyprotein 1a and the four genes coding for major structural proteins spike (S), small envelope (E), membrane (M) and nucleocapsid (N), six to eight additional proteins have been predicted depending upon the strain analyzed. Their lengths range between 61 and 274 amino acids. Our method also suggests that polyprotein 1ab, polyprotein 1a, S, M and N are proteins of viral origin and others are of prokaryotic. Putative functions of all predicted protein-coding genes have been suggested using conserved peptides present in their open reading frames.

Availability: Detailed results of GeneDecipher analysis of all the 18 strains of SARS-CoV genomes are available at http://www.igib.res.in/sarsanalysis.html

Contact: skb{at}igib.res.in

* To whom correspondence should be addressed.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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