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

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 regionspecific reliability is assessed by producing multiple sequence alignments in different sequence contexts followed by the analysis of the consistency of ali...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Mindaugas Margelevicius, Ceslovas Venclovas
• Keywords: BMCBI 2005, Protein Sequence Alignments, Proteins, Sequence Alignments