NdPASA: a pairwise sequence alignment server for distantly related proteins | Zendy

Wei Li | Zendy; Junwen Wang | Zendy; Jin An Feng | Zendy

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NdPASA: a pairwise sequence alignment server for distantly related proteins

Author(s) -

Wei Li,

Junwen Wang,

Jin An Feng

Publication year - 2005

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti619

Subject(s) - pairwise comparison , sequence (biology) , sequence alignment , computer science , multiple sequence alignment , computational biology , biology , peptide sequence , genetics , artificial intelligence , gene

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.

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