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

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Intermediate sequences increase the detection of homology between sequences

Cited 153 times inthomson ciCited 174 times inthomson ci
Title
Intermediate sequences increase the detection of homology between sequences
Other Titles
Intermediate sequences increase the detection of homology between sequences.
Author
Bhak, Jong HwaTeichmann, Sarah A.Hubbard, TimChothia, Cyrus
Keywords
HIDDEN MARKOV-MODELS; PROTEINS; ALIGNMENT; DATABASE; SENSITIVITY; BIOLOGY
Issue Date
1997-10
Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
Citation
JOURNAL OF MOLECULAR BIOLOGY, v.273, no.1, pp.349 - 354
Abstract
Two homologous sequences, which have diverged beyond the point where their homology can be recognised by a simple direct comparison, can be related through a third sequence that is suitably intermediate between the two. High scores, for a sequence match between the first and third sequences and between the second and the third sequences, imply that the first and second sequences are related even though their own match score is low. We have tested the usefulness of this idea using a database that contains the sequences of 971 protein domains whose structures are known and whose residue identities with each other are some 40% or less (PDB40D). On the basis of sequence and structural information, 2143 pairs of these sequences are known to have an evolutionary relationship. FASTA, in an all-against-all comparison of the sequences in the database, detected 320 (15%) of these relationships as well as three false positives (i.e. 1% error rate). Using intermediate sequences found by FASTA matches of PDB40D sequences to those in the large non-redundant OWL database we could detect 550 evolutionary relationships with an error rate of 1%. This means the intermediate sequence procedure increases the ability to recognise the evolutionary relationships amongst the PDB40D sequences by 70%. (C) 1997 Academic Press Limited
URI
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DOI
10.1006/jmbi.1997.1288
ISSN
0022-2836
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BME_Journal Papers
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