A statistical score for assessing the quality of multiple sequence alignments

Background: Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc. Although the automatic construction of a multiple sequence alignment for a set of remotely related sequences cause a very challenging and error-prone task, many downstream analyses still rely heavily on the accuracy of the alignments. Results: To address the need for an objective evaluation framework, we introduce a statistical score that assesses the quality of a given multiple sequence alignment. The quality assessment is based on counting the number of significantly conserved positions in the alignment using importance sampling method in conjunction with statistical profile analysis framework. We first evaluate a novel objective function used in the alignment quality score for measuring the positional conservation. The results for the Src homology 2 (SH2) domai...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka
• Keywords: Alignment Quality Score, BMCBI 2006, Multiple Sequence Alignment, Sequence Alignment Programs