MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

Publication type:
Journal article
Metadata:
Autoren
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000280703500006&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1093/bioinformatics/btq338
eISSN
1460-2059
Externe Identifier
  • Clarivate Analytics Document Solution ID: 636BS
  • PubMed Identifier: 20576627
ISSN
1367-4803
Ausgabe der Veröffentlichung
16
Zeitschrift
BIOINFORMATICS
Paginierung
1958 - 1964
Datum der Veröffentlichung
2010
Status
Published
Titel
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
Sub types
  • Article
Ausgabe der Zeitschrift
26

Data source: Web of Science (Lite)

Other metadata sources:
Abstract
<jats:title>Abstract</jats:title> <jats:p>Motivation: Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate multiple alignments is still a challenge.</jats:p> <jats:p>Results: We present MSAProbs, a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Furthermore, two critical bioinformatics techniques, namely weighted probabilistic consistency transformation and weighted profile–profile alignment, are incorporated to improve alignment accuracy. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners.</jats:p> <jats:p>Availability: The source code of MSAProbs, written in C++, is freely and publicly available from http://msaprobs.sourceforge.net.</jats:p> <jats:p>Contact:  liuy0039@ntu.edu.sg</jats:p>
Autoren
DOI
10.1093/bioinformatics/btq338
eISSN
1367-4811
ISSN
1367-4803
Ausgabe der Veröffentlichung
16
Zeitschrift
Bioinformatics
Sprache
en
Online publication date
2010
Paginierung
1958 - 1964
Datum der Veröffentlichung
2010
Status
Published
Herausgeber
Oxford University Press (OUP)
Herausgeber URL
http://dx.doi.org/10.1093/bioinformatics/btq338
Datum der Datenerfassung
2023
Titel
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
Ausgabe der Zeitschrift
26

Data source: Crossref

Abstract
<h4>Motivation</h4>Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate multiple alignments is still a challenge.<h4>Results</h4>We present MSAProbs, a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Furthermore, two critical bioinformatics techniques, namely weighted probabilistic consistency transformation and weighted profile-profile alignment, are incorporated to improve alignment accuracy. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners.<h4>Availability</h4>The source code of MSAProbs, written in C++, is freely and publicly available from http://msaprobs.sourceforge.net.
Addresses
  • School of Computer Engineering, Nanyang Technological University, Singapore. liuy0039@ntu.edu.sg
Autoren
DOI
10.1093/bioinformatics/btq338
eISSN
1367-4811
Externe Identifier
  • PubMed Identifier: 20576627
Open access
false
ISSN
1367-4803
Ausgabe der Veröffentlichung
16
Zeitschrift
Bioinformatics (Oxford, England)
Schlüsselwörter
  • Probability
  • Markov Chains
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Computational Biology
  • Amino Acid Sequence
  • Algorithms
  • Software
Sprache
eng
Medium
Print-Electronic
Online publication date
2010
Paginierung
1958 - 1964
Datum der Veröffentlichung
2010
Status
Published
Datum der Datenerfassung
2010
Titel
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
26

Data source: Europe PubMed Central

Abstract
MOTIVATION: Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate multiple alignments is still a challenge. RESULTS: We present MSAProbs, a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Furthermore, two critical bioinformatics techniques, namely weighted probabilistic consistency transformation and weighted profile-profile alignment, are incorporated to improve alignment accuracy. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners. AVAILABILITY: The source code of MSAProbs, written in C++, is freely and publicly available from http://msaprobs.sourceforge.net.
Autoren
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/20576627
DOI
10.1093/bioinformatics/btq338
eISSN
1367-4811
Ausgabe der Veröffentlichung
16
Zeitschrift
Bioinformatics
Schlüsselwörter
  • Algorithms
  • Amino Acid Sequence
  • Computational Biology
  • Markov Chains
  • Probability
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Software
Sprache
eng
Country
England
Paginierung
1958 - 1964
PII
btq338
Datum der Veröffentlichung
2010
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2010
Titel
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
26

Data source: PubMed

Autoren
Zeitschrift
Bioinform.
Artikelnummer
16
Paginierung
1958 - 1964
Datum der Veröffentlichung
2010
Titel
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.
Ausgabe der Zeitschrift
26

Data source: DBLP

Beziehungen:
Property of

Tools