The multiple alignment problem consists of inferring all homologous characters among multiple biological sequences. The characters may consist of single nucleotides, amino acids, genes, or any sequence segments that may share an evolutionary origin. Multiple alignments may be used to study which sequences have been conserved over time. This is the starting point of comparative genomics and molecular phylogenetics studies.
Multiple sequence alignment programs and techniques
A common approach for multiple sequence alignment is to progressively align sequences using a guide tree. Initially, each sequence at the leaves is represented as a trivial alignment of a single sequence. Then, at each internal node, the alignments at its children are merged into an alignment of the alignments. At the end, the root contains an alignment on all the sequences. This is called progressive alignment.
There are many computer programs to produce multiple sequence alignments starting with a collection of unaligned sequences (ClustalW, DIALIGN, MAVID, TBA, T-Coffee) and to represent graphically those alignments (ClustalW, Belvu).
References
Survey articles
- Duret, L. (2000). "Multiple alignment for structural functional or phylogenetic analyses of homologous sequences". In D. Higgins and W. Taylor (ed.). Bioinformatics sequence structure and databanks. Oxford: Oxford University Press.
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- Notredame, C. (2002). "Recent progresses in multiple sequence alignment: a survey". Pharmacogenomics. 31 (1): 131 -- 144.
- Thompson, J. D. (1999). "A comprehensive comparison of multiple sequence alignment programs". Nucleic Acids Research. 27 (13): 12682--2690.
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