PSAR-align: Improving Multiple Sequence Alignment Using Probabilistic Sampling

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2013 Nov 14

PMID 24222208

Citations 5

Authors

Jaebum Kim

Jian Ma

Affiliations

Soon will be listed here.

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.

Citing Articles

LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation.

Maldonado E, Antunes A BMC Bioinformatics. 2020; 20(1):739.

PMID: 31888452 PMC: 6937843. DOI: 10.1186/s12859-019-3292-5.

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments.

Ali R, Bogusz M, Whelan S Mol Biol Evol. 2019; 36(10):2340-2351.

PMID: 31209473 PMC: 6933875. DOI: 10.1093/molbev/msz142.

seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.

Jandrasits C, Dabrowski P, Fuchs S, Renard B BMC Genomics. 2018; 19(1):47.

PMID: 29334898 PMC: 5769345. DOI: 10.1186/s12864-017-4401-3.

Portable and Error-Free DNA-Based Data Storage.

Tabatabaei Yazdi S, Gabrys R, Milenkovic O Sci Rep. 2017; 7(1):5011.

PMID: 28694453 PMC: 5503945. DOI: 10.1038/s41598-017-05188-1.

Alignathon: a competitive assessment of whole-genome alignment methods.

Earl D, Nguyen N, Hickey G, Harris R, Fitzgerald S, Beal K Genome Res. 2014; 24(12):2077-89.

PMID: 25273068 PMC: 4248324. DOI: 10.1101/gr.174920.114.

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