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. 2014 Apr 1;30(7):1010-2.
doi: 10.1093/bioinformatics/btt636. Epub 2013 Nov 12.

PSAR-align: improving multiple sequence alignment using probabilistic sampling

Jaebum Kim  1 , Jian Ma
Affiliations

PSAR-align: improving multiple sequence alignment using probabilistic sampling

Jaebum Kim et al. Bioinformatics. .

Abstract

Summary: We developed PSAR-Align, a multiple sequence realignment tool that can refine a given multiple sequence alignment based on suboptimal alignments generated by probabilistic sampling. Our evaluation demonstrated that PSAR-Align is able to improve the results from various multiple sequence alignment tools.

Availability and implementation: The PSAR-Align source code (implemented mainly in C++) is freely available for download at http://bioen-compbio.bioen.illinois.edu/PSAR-Align.

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Figures

Fig. 1.
Fig. 1.
Overview of the PSAR-Align algorithm. Given input MSA, PSAR-Align first samples SAs (A and B). These SAs are analyzed by a pair of sequences at a time (C), and posterior probabilities of aligning two residues from two different sequences are computed (D). By using these probabilities, PSAR-Align finds the revised alignment based on the maximization technique of expected accuracy (E)
See this image and copyright information in PMC

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