Title: SnS-Align: a graphic tool for alignment of distantly related proteins

Authors: Ganiraju Manyam, Ancha Baranova, Mikhail Skoblov, Rakesh K. Mishra

Addresses: Department of Molecular and Microbiology, College of Science, George Mason University, PW2 University Blvd., Manassas, VA 20110, USA. ' Department of Molecular and Microbiology, College of Science, George Mason University, PW2 University Blvd., Manassas, VA 20110, USA. ' Research Center for Medical Genetics, RAMS, Moskvorechie Str., 1, Moscow, Russian Federation. ' Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India

Abstract: Genomic sequences for many animal species are now available in the public domain. Protein similarity search in evolutionarily distant organisms by sequence comparison often turns out to be difficult. Here, we present the Structure and Sequence Alignment (SnS-Align) tool that graphically presents pairwise local alignment of sandwiched protein sequences, a hybrid of the primary protein sequence and its secondary structure. The utility of the tool is demonstrated by sample analysis of the gap junction protein superfamily of innexins/pannexins and the classic myoglobin family. SnS-Align can also be used for demarcation of the structurally conserved domains within superfamilies of paralogous genes.

Keywords: sequence alignment; structure alignment; remote homology detection; sandwiched protein sequence comparison; pairwise sequence alignment; structurally conserved domains; SnS-Align; distantly related proteins; bioinformatics; paralogous genes; DNA sequences.

DOI: 10.1504/IJBRA.2009.029045

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.6, pp.663 - 673

Received: 24 Dec 2007
Accepted: 16 Apr 2009
Published online: 29 Oct 2009 *

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