NdPASA: A pairwise sequence alignment server for distantly related proteins

Wei Li; Junwen Wang; Jin An Feng

doi:10.1093/bioinformatics/bti619

NdPASA: A pairwise sequence alignment server for distantly related proteins

Wei Li, Junwen Wang, Jin An Feng

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Research output: Contribution to journal › Article › peer-review

2 Scopus citations

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.

Original language	English (US)
Pages (from-to)	3803-3805
Number of pages	3
Journal	Bioinformatics
Volume	21
Issue number	19
DOIs	https://doi.org/10.1093/bioinformatics/bti619
State	Published - Oct 2005

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bti619

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title = "NdPASA: A pairwise sequence alignment server for distantly related proteins",

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.",

author = "Wei Li and Junwen Wang and Feng, {Jin An}",

note = "Funding Information: The authors would like to thank members of the Feng laboratory for helpful discussions. The authors also thank the American Cancer Society for the financial support (PRG9926301GMC) and the commonwealth of Pennsylvania for the appropriation.",

year = "2005",

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doi = "10.1093/bioinformatics/bti619",

language = "English (US)",

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T2 - A pairwise sequence alignment server for distantly related proteins

AU - Li, Wei

AU - Wang, Junwen

AU - Feng, Jin An

N1 - Funding Information: The authors would like to thank members of the Feng laboratory for helpful discussions. The authors also thank the American Cancer Society for the financial support (PRG9926301GMC) and the commonwealth of Pennsylvania for the appropriation.

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N2 - 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.

AB - 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.

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NdPASA: A pairwise sequence alignment server for distantly related proteins

Abstract

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