PSAR-align: improving multiple sequence alignment using probabilistic sampling

Jaebum Kim; Jian Ma

doi:10.1093/bioinformatics/btt636

PSAR-align: improving multiple sequence alignment using probabilistic sampling

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

Authors

Jaebum Kim¹, Jian Ma

Affiliation

¹ Department of Animal Biotechnology, UBITA Center for Biotechnology Research (CBRU), Konkuk University, Seoul 143-701, Korea, Department of Bioengineering and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
High-Throughput Nucleotide Sequencing / methods*
Probability
Sequence Alignment
Software*

Grants and funding

HG006464/HG/NHGRI NIH HHS/United States