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Bioinformatics Advance Access originally published online on August 16, 2005
Bioinformatics 2005 21(19):3803-3805; 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{at}oxfordjournals.org

NdPASA: a pairwise sequence alignment server for distantly related proteins

Wei Li 1, Junwen Wang 2,{dagger} and Jin-An Feng 1,2,*

1Department of Chemistry, Temple University Philadelphia, PA 19122, USA
2Center for Biotechnology, Temple University Philadelphia, PA 19122, USA

*To whom correspondence should be addressed at Department of chemistry, Temple University, 1901 N. 13th street, Philadelphia, PA19122, USA

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

Contact: feng{at}temple.edu

Received on May 9, 2005; revised on July 13, 2005; accepted on August 8, 2005

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