Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote . . . (1998)
| Citations: | 146 - 14 self |
BibTeX
@MISC{Park98sequencecomparisons,
author = {Jong Park and Kevin Karplus and Christian Barrett and Richard Hughey and David Haussler and Tim Hubbard and Cyrus Chothia},
title = {Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote . . . },
year = {1998}
}
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Abstract
The sequences of related proteins can diverge beyond the point where their relationship can be recognised by pairwise sequence comparisons. In attempts to overcome this limitation, methods have been developed that use as a query, not a single sequence, but sets of related sequences or a representation of the characteristics shared by related sequences. Here we describe an assessment of three of these methods: the SAM-T98 implementation of a hidden Markov model procedure; PSI-BLAST; and the intermediate sequence search (ISS) procedure. We determined the extent to which these procedures can detect evolutionary relationships between the members of the sequence database PDBD40-J. This database, derived from the structural classification of proteins (SCOP), contains the sequences of proteins of known structure whose sequence identities with each other are 40 % or less. The evolutionary relationships that exist between those that have low sequence identities were found by the examination of their structural details and, in many cases, their functional
