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.
Keywords
Multiple sequence alignmentSequence (biology)Computer scienceAlgorithmPartition (number theory)Structural alignmentHeuristicHidden Markov modelSmith–Waterman algorithmMarkov chainSequence alignmentArtificial intelligenceTheoretical computer scienceMathematicsMachine learningCombinatoricsBiologyPeptide sequenceGenetics
MeSH Terms
AlgorithmsComputational BiologyMarkov ChainsProteinsSequence AlignmentSoftware
Affiliated Institutions
Related Publications
Accelerated Profile HMM Searches
Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, pr...
Profile hidden Markov models.
Abstract The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-spe...
HH-suite3 for fast remote homology detection and deep protein annotation
Abstract Background HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignme...
PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information
Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remai...
ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches
There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel...
Publication Info
- Year
- 2013
- Type
- article
- Volume
- 1079
- Pages
- 211-218
- Citations
- 20
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
20
OpenAlex
4
Influential
16
CrossRef
Cite This
Yongchao Liu,
Bertil Schmidt
(2013).
Multiple Protein Sequence Alignment with MSAProbs.
Methods in molecular biology
, 1079
, 211-218.
https://doi.org/10.1007/978-1-62703-646-7_14
Identifiers
- DOI
- 10.1007/978-1-62703-646-7_14
- PMID
- 24170405