Open Access
Bioinformatics, volume 21, issue 7, pages 951-960
Protein homology detection by HMM-HMM comparison
Publication type: Journal Article
Publication date: 2004-11-05
Journal:
Bioinformatics
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 5.8
ISSN: 13674803, 13674811, 14602059
Biochemistry
Computer Science Applications
Molecular Biology
Statistics and Probability
Computational Mathematics
Computational Theory and Mathematics
Abstract
Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution.We have generalized the alignment of protein sequences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile HMMs. We present a method for detecting distant homologous relationships between proteins based on this approach. The method (HHsearch) is benchmarked together with BLAST, PSI-BLAST, HMMER and the profile-profile comparison tools PROF_SIM and COMPASS, in an all-against-all comparison of a database of 3691 protein domains from SCOP 1.63 with pairwise sequence identities below 20%.Sensitivity: When the predicted secondary structure is included in the HMMs, HHsearch is able to detect between 2.7 and 4.2 times more homologs than PSI-BLAST or HMMER and between 1.44 and 1.9 times more than COMPASS or PROF_SIM for a rate of false positives of 10%. Approximately half of the improvement over the profile-profile comparison methods is attributable to the use of profile HMMs in place of simple profiles. Alignment quality: Higher sensitivity is mirrored by an increased alignment quality. HHsearch produced 1.2, 1.7 and 3.3 times more good alignments ('balanced' score >0.3) than the next best method (COMPASS), and 1.6, 2.9 and 9.4 times more than PSI-BLAST, at the family, superfamily and fold level, respectively.Speed: HHsearch scans a query of 200 residues against 3691 domains in 33 s on an AMD64 2GHz PC. This is 10 times faster than PROF_SIM and 17 times faster than COMPASS.
Top-30
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IEEE
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19 publications, 0.92%
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- We do not take into account publications without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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TY - JOUR
DO - 10.1093/bioinformatics/bti125
UR - https://doi.org/10.1093/bioinformatics/bti125
TI - Protein homology detection by HMM-HMM comparison
T2 - Bioinformatics
AU - Söding, Johannes
PY - 2004
DA - 2004/11/05 00:00:00
PB - Oxford University Press
SP - 951-960
IS - 7
VL - 21
SN - 1367-4803
SN - 1367-4811
SN - 1460-2059
ER -
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@article{2004_Söding,
author = {Johannes Söding},
title = {Protein homology detection by HMM-HMM comparison},
journal = {Bioinformatics},
year = {2004},
volume = {21},
publisher = {Oxford University Press},
month = {nov},
url = {https://doi.org/10.1093/bioinformatics/bti125},
number = {7},
pages = {951--960},
doi = {10.1093/bioinformatics/bti125}
}
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Söding, Johannes. “Protein homology detection by HMM-HMM comparison.” Bioinformatics, vol. 21, no. 7, Nov. 2004, pp. 951-960. https://doi.org/10.1093/bioinformatics/bti125.