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Open Access Software

PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability

Mindaugas Margelevičius and Česlovas Venclovas*

Author Affiliations

Institute of Biotechnology, Graičiūno 8, LT-02241 Vilnius, Lithuania

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BMC Bioinformatics 2005, 6:185  doi:10.1186/1471-2105-6-185

Published: 21 July 2005

Abstract

Background

Protein sequence alignments have become indispensable for virtually any evolutionary, structural or functional study involving proteins. Modern sequence search and comparison methods combined with rapidly increasing sequence data often can reliably match even distantly related proteins that share little sequence similarity. However, even highly significant matches generally may have incorrectly aligned regions. Therefore when exact residue correspondence is used to transfer biological information from one aligned sequence to another, it is critical to know which alignment regions are reliable and which may contain alignment errors.

Results

PSI-BLAST-ISS is a standalone Unix-based tool designed to delineate reliable regions of sequence alignments as well as to suggest potential variants in unreliable regions. The region-specific reliability is assessed by producing multiple sequence alignments in different sequence contexts followed by the analysis of the consistency of alignment variants. The PSI-BLAST-ISS output enables the user to simultaneously analyze alignment reliability between query and multiple homologous sequences. In addition, PSI-BLAST-ISS can be used to detect distantly related homologous proteins. The software is freely available at: http://www.ibt.lt/bioinformatics/iss webcite.

Conclusion

PSI-BLAST-ISS is an effective reliability assessment tool that can be useful in applications such as comparative modelling or analysis of individual sequence regions. It favorably compares with the existing similar software both in the performance and functional features.