NDLI: Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies

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Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies

Content Provider	Scilit
Author	May, Alex C. W.
Copyright Year	2009
Description	Journal: Protein Science It is often possible to identify sequence motifs that characterize a protein family in terms of its fold and/or function from aligned protein sequences. Such motifs can be used to search for new family members. Partitioning of sequence alignments into regions of similar amino acid variability is usually done by hand. Here, I present a completely automatic method for this purpose: one that is guaranteed to produce globally optimal solutions at all levels of partition granularity. The method is used to compare the tempo of sequence diversity across reliable three-dimensional (3D) structure-based alignments of 209 protein families (HOMSTRAD) and that for 69 superfamilies (CAMPASS). (The mean alignment length for HOMSTRAD and CAMPASS are very similar.) Surprisingly, the optimal segmentation distributions for the closely related proteins and distantly related ones are found to be very similar. Also, optimal segmentation identifies an unusual protein superfamily. Finally, protein 3D structure clues from the tempo of sequence diversity across alignments are examined. The method is general, and could be applied to any area of comparative biological sequence and 3D structure analysis where the constraint of the inherent linear organization of the data imposes an ordering on the set of objects to be clustered.
Related Links	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373737/pdf
Ending Page	2835
Page Count	11
Starting Page	2825
e-ISSN	1469896X
DOI	10.1110/ps.0211202
Journal	Protein Science
Issue Number	12
Volume Number	11
Language	English
Publisher	Wiley-Blackwell
Publisher Date	2009-04-13
Access Restriction	Open
Subject Keyword	Journal: Protein Science Mathematical and Computational Biology Multiple Sequence Alignment Computational Biology Sequence Alignment Sequence Motif Protein Superfamily Conserved Sequence
Content Type	Text
Resource Type	Article

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