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BMCBI
2004

Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model

8 years 12 months ago
Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model
Background: Certain protein families are highly conserved across distantly related organisms and belong to large and functionally diverse superfamilies. The patterns of conservation present in these protein sequences presumably are due to selective constraints maintaining important but unknown structural mechanisms with some constraints specific to each family and others shared by a larger subset or by the entire superfamily. To exploit these patterns as a source of functional information, we recently devised a statistically based approach called contrast hierarchical alignment and interaction network (CHAIN) analysis, which infers the strengths of various categories of selective constraints from co-conserved patterns in a multiple alignment. The power of this approach strongly depends on the quality of the multiple alignments, which thus motivated development of theoretical concepts and strategies to improve alignment of conserved motifs within large sets of distantly related sequenc...
Andrew F. Neuwald, Jun S. Liu
Added 16 Dec 2010
Updated 16 Dec 2010
Type Journal
Year 2004
Where BMCBI
Authors Andrew F. Neuwald, Jun S. Liu
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