Multiple protein sequence alignment with MSAProbs - PubMed (original) (raw)
Multiple protein sequence alignment with MSAProbs
Yongchao Liu et al. Methods Mol Biol. 2014.
Abstract
Multiple sequence alignment (MSA) generally constitutes the foundation of many bioinformatics studies involving functional, structural, and evolutionary relationship analysis between sequences. As a result of the exponential computational complexity of the exact approach to producing optimal multiple alignments, the majority of state-of-the-art MSA algorithms are designed based on the progressive alignment heuristic. In this chapter, we outline MSAProbs, a parallelized MSA algorithm for protein sequences based on progressive alignment. To achieve high alignment accuracy, this algorithm employs a hybrid combination of a pair hidden Markov model and a partition function to calculate posterior probabilities. Furthermore, we provide some practical advice on the usage of the algorithm.
Similar articles
- MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.
Liu Y, Schmidt B, Maskell DL. Liu Y, et al. Bioinformatics. 2010 Aug 15;26(16):1958-64. doi: 10.1093/bioinformatics/btq338. Epub 2010 Jun 23. Bioinformatics. 2010. PMID: 20576627 - Multiple sequence alignment using Probcons and Probalign.
Roshan U. Roshan U. Methods Mol Biol. 2014;1079:147-53. doi: 10.1007/978-1-62703-646-7_9. Methods Mol Biol. 2014. PMID: 24170400 - ProbPFP: a multiple sequence alignment algorithm combining hidden Markov model optimized by particle swarm optimization with partition function.
Zhan Q, Wang N, Jin S, Tan R, Jiang Q, Wang Y. Zhan Q, et al. BMC Bioinformatics. 2019 Nov 25;20(Suppl 18):573. doi: 10.1186/s12859-019-3132-7. BMC Bioinformatics. 2019. PMID: 31760933 Free PMC article. - Multiple sequence alignment.
Edgar RC, Batzoglou S. Edgar RC, et al. Curr Opin Struct Biol. 2006 Jun;16(3):368-73. doi: 10.1016/j.sbi.2006.04.004. Epub 2006 May 5. Curr Opin Struct Biol. 2006. PMID: 16679011 Review. - Protein multiple sequence alignment.
Do CB, Katoh K. Do CB, et al. Methods Mol Biol. 2008;484:379-413. doi: 10.1007/978-1-59745-398-1_25. Methods Mol Biol. 2008. PMID: 18592193 Review.
Cited by
- The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor.
Catchpole RJ, Forterre P. Catchpole RJ, et al. Mol Biol Evol. 2019 Dec 1;36(12):2737-2747. doi: 10.1093/molbev/msz180. Mol Biol Evol. 2019. PMID: 31504731 Free PMC article. - Deciphering key features in protein structures with the new ENDscript server.
Robert X, Gouet P. Robert X, et al. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W320-4. doi: 10.1093/nar/gku316. Epub 2014 Apr 21. Nucleic Acids Res. 2014. PMID: 24753421 Free PMC article. - Tuned SMC Arms Drive Chromosomal Loading of Prokaryotic Condensin.
Bürmann F, Basfeld A, Vazquez Nunez R, Diebold-Durand ML, Wilhelm L, Gruber S. Bürmann F, et al. Mol Cell. 2017 Mar 2;65(5):861-872.e9. doi: 10.1016/j.molcel.2017.01.026. Epub 2017 Feb 23. Mol Cell. 2017. PMID: 28238653 Free PMC article. - Ancestral State Reconstruction of the Apoptosis Machinery in the Common Ancestor of Eukaryotes.
Klim J, Gładki A, Kucharczyk R, Zielenkiewicz U, Kaczanowski S. Klim J, et al. G3 (Bethesda). 2018 May 31;8(6):2121-2134. doi: 10.1534/g3.118.200295. G3 (Bethesda). 2018. PMID: 29703784 Free PMC article. - Comparative Genomics of Closely Related Tetragenococcus halophilus Strains Elucidate the Diversity and Microevolution of CRISPR Elements.
Matsutani M, Wakinaka T, Watanabe J, Tokuoka M, Ohnishi A. Matsutani M, et al. Front Microbiol. 2021 Jun 18;12:687985. doi: 10.3389/fmicb.2021.687985. eCollection 2021. Front Microbiol. 2021. PMID: 34220781 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials