BROWSE

Related Researcher

Author's Photo

Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

ITEM VIEW & DOWNLOAD

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods

Cited 357 times inthomson ciCited 392 times inthomson ci
Title
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
Other Titles
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.
Author
Bhak, Jong HwaKarplus, KevinBarrett, ChristianHughey, RichardHaussler, DavidHubbard, TimChothia, Cyrus
Keywords
protein homology; intermediate sequence search; hidden Markov models; SAM-T98; PSI-BLAST; SCOP
Issue Date
1998-12
Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
Citation
JOURNAL OF MOLECULAR BIOLOGY, v.284, no.4, pp.1201 - 1210
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 features. For nine false positive predictions out of a possible 432,680, i.e. at a false positive rate of about 1/50,000, SAM-T98 found 35% of the true homologous relationships in PDBD40-J, whilst PSI-BLAST found 30% and ISS found 25%. Overall, this is about twice the number of PDBD40-J relations that can be detected by the pairwise comparison procedures FASTA (17%) and GAP-BLAST (15%). For distantly related sequences in PDBD40-J, those pairs whose sequence identity is less than 30%, SAM-T98 and PSI-BLAST detect three times the number of relationships found by the pairwise methods. (C) 1998 Academic Press
URI
Go to Link
DOI
10.1006/jmbi.1998.2221
ISSN
0022-2836
Appears in Collections:
BME_Journal Papers
Files in This Item:
1-s2.0-S0022283698922215-main.pdf Download

find_unist can give you direct access to the published full text of this article. (UNISTARs only)

Show full item record

qrcode

  • mendeley

    citeulike

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

MENU