Abstract Motivation The recent out break of Severe Acute Respiratory Syndrome caused by.pdf

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Abstract Motivation The recent out break of Severe Acute Respiratory Syndrome caused by.pdf

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Abstract Motivation The recent out break of Severe Acute Respiratory Syndrome caused by

1Recognition and analysis of protein coding genes in Severe Acute Respiratory Syndrome associated Coronavirus Ramakant Sharma # , Jitendra Kumar Maheshwari # , Tulika Prakash, Debasis Dash, Samir K.Brahmachari * Institute of Genomics and Integrative Biology CSIR, Mall Road, Delhi 110 007, India # Both authors have contributed equally *Address for Correspondence: Prof. Samir K. Brahmachari Institute of Genomics and Integrative Biology (Formerly Centre for Biochemical Technology) Mall Road, Delhi 110 007, India Tel: 91-11-2766-7578 Fax: 91-11-2766-7471 Email: skb@igib.res.in Bioinformatics Advance Access published February 5, 2004 Copyright (c) 2004 Oxford University Press 2Abstract: Motivation: The recent out break of Severe Acute Respiratory Syndrome caused by SARS coronavirus has necessitated 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 1ab*, polyprotein 1a and the four genes coding for major structural proteins spike(S), small envelope (E), membrane (M), and nucleocapsid (N), 6 to 8 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, spike (S), membrane (M), Nucleocapsid (N) are proteins of viral origin and others are of prokaryotic. Putative functions of all predicted protein coding genes have been suggested using conserved