Multiple sequence alignment: Difference between revisions

Revision as of 23:13, 10 September 2006

Revision as of 03:42, 12 September 2006

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Another iterative program, DIALIGN, takes an unusual approach of focusing narrowly on local alignments between sub-segments or [[sequence motif]]s without introducing a gap penalty.<ref name="brudno">Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B. (2003) Fast and sensitive multiple alignment of large genomic sequences. ''BMC Bioinformatics'' 4:66.</ref> The alignment of individual motifs is then achieved with a matrix representation similar to a dot-matrix plot in a pairwise alignment. An alternative method that uses fast local alignments as anchor points or "seeds" for a slower global-alignment procedure is implemented in the [http://dialign.gobics.de/chaos-dialign-submission CHAOS/DIALIGN] suite.<ref name="brudno">Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B. (2003) Fast and sensitive multiple alignment of large genomic sequences ''BMC Bioinformatics'' 4:66.</ref>

A third popular iteration-based method called [http://www.drive5.com/muscle/ MUSCLE] (multiple sequence alignment by log-expectation) improves on progressive methods with a more accurate distance measure to assess the relatedness of two sequences.<ref name="edgar">Edgar RC. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput. ''Nucleic Acids Research'' 32(5), 1792-97.</ref> The distance measure is updated between iteration stages (although, in its original form, MUSCLE contained only 2-3 iterations depending on whether refinement was enabled). A web portal and download site is available at [http://www.drive5.com/muscle/ MUSCLE].

==Hidden Markov models==