Multiple sequence alignment: Difference between revisions

Revision as of 07:48, 10 September 2006

Revision as of 22:44, 10 September 2006

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A variety of subtly different iteration methods have been implemented and made available in software packages; reviews and comparisons have been useful but generally refrain from choosing a "best" technique.<ref name="hirosawa">Hirosawa M, Totoki Y, Hoshida M, Ishikawa M. (1995). Comprehensive study on iterative algorithms of multiple sequence alignment. ''Comput Appl Biosci'' 11:13-18.</ref> The software package [http://prrn.hgc.jp/ PRRN/PRRP] uses a [[hill-climbing algorithm]] to optimize its MSA alignment score<ref name="gotoh">Gotoh O. (1996). Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. ''J Mol Biol'' 264(4):823-38.</ref> and iteratively corrects both alignment weights and locally divergent or "gappy" regions of the growing MSA.<ref name="mount">Mount DM. (2004). Bioinformatics: Sequence and Genome Analysis 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.</ref> PRRP performs best when refining an alignment previously constructed by a faster method.<ref name="mount">

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. DIALIGNAn isalternative alsomethod availablethat uses fast local alignments as anchor points or "seeds" for a webslower portalglobal-alignment procedure is implemented in atthe [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 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].