Journal
BRIEFINGS IN BIOINFORMATICS
Volume 17, Issue 6, Pages 1009-1023Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbv099
Keywords
multiple sequence alignments; protein alignments; alignment benchmarks; alignment reliability measures; RNA alignments; DNA alignments
Funding
- Spanish Ministry of Economy and Competitiveness [BFU2014-55062-P]
- Secretariat of Universities and Research, Dept. of Economy and Knowledge of the Government of Catalonia [2014 SGR 1114]
- la Caixa International Fellowship Programme for a predoctoral fellowship at the CRG
- Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa [SEV-2012-0208]
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This review provides an overview on the development of Multiple sequence alignment (MSA) methods and their main applications. It is focused on progress made over the past decade. The three first sections review recent algorithmic developments for protein, RNA/DNA and genomic alignments. The fourth section deals with benchmarks and explores the relationship between empirical and simulated data, along with the impact on method developments. The last part of the review gives an overview on available MSA local reliability estimators and their dependence on various algorithmic properties of available methods.
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