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Bioinformatics Advance Access published online on August 16, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti619
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 9, 2005
Revised July 13, 2005
Accepted August 8, 2005

Applications note

NdPASA: a pairwise sequence alignment server for distantly related proteins

Wei Li 1, Junwen Wang 2, and Jin-an Feng 3*

1 Department of Chemistry, Temple University, Philadelphia, PA 19122
2 Center for Biotechnology, Temple University, Philadelphia, PA 19122; Current address: Center for Bioinformatics and Department of Genetics, University of Pennsylvania, PA 19104, USA
3 Department of Chemistry, Temple University, Philadelphia, PA 19122; Center for Biotechnology, Temple University, Philadelphia, PA 19122

* To whom correspondence should be addressed.
Jin-an Feng, E-mail: feng{at}astro.temple.edu


  Abstract

Summary: NdPASA is a web server specifically designed to optimize sequence alignment between distantly related proteins. The program integrates structure information of the template sequence into a global alignment algorithm by employing neighbor-dependent propensities of amino acids as a unique parameter for alignment. NdPASA optimizes alignment by evaluating the likelihood of a residue pair in the query sequence matching against a corresponding residue pair adopting a particular secondary structure in the template sequence. NdPASA is most effective in aligning homologous proteins sharing low percentage of sequence identity. The server is designed to aid homologous protein structure modeling. A PSI-BLAST search engine was implemented to help users identify template candidates that are most appropriate for modeling the query sequences.

Availability: (http://guanyin.chem.temple.edu).


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