PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences.

ABSTRACT: Accurate tools for multiple sequence alignment (MSA) are essential for comparative studies of the function and structure of biological sequences. However, it is very challenging to develop a computationally efficient algorithm that can consistently predict accurate alignments for various types of sequence sets. In this article, we introduce PicXAA (Probabilistic Maximum Accuracy Alignment), a probabilistic non-progressive alignment algorithm that aims to find protein alignments with maximum expected accuracy. PicXAA greedily builds up the multiple alignment from sequence regions with high local similarities, thereby yielding an accurate global alignment that effectively grasps the local similarities among sequences. Evaluations on several widely used benchmark sets show that PicXAA constan

SUBMITTER: Sahraeian SM 

PROVIDER: S-EPMC2926610 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature