Physicochemical property distributions for accurate and rapid pairwise protein homology detection

Webb-Robertson, Bobbie-Jo M.; Ratuiste, Kyle G.; Oehmen, Christopher S.

doi:10.1186/1471-2105-11-145

Physicochemical property distributions for accurate and rapid pairwise protein homology detection

Journal Article · Fri Mar 19 00:00:00 EDT 2010 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-11-145· OSTI ID:1626267

Webb-Robertson, Bobbie-Jo M. ^[1]; Ratuiste, Kyle G. ^[2]; Oehmen, Christopher S. ^[3]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Computational Biology and Bioinformatics; DOE/OSTI
Gonzaga Univ., Spokane, WA (United States). Dept. of Chemistry
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Computational Biology and Bioinformatics

Background: The challenge of remote homology detection is that many evolutionarily related sequences have very little similarity at the amino acid level. Kernel-based discriminative methods, such as support vector machines (SVMs), that use vector representations of sequences derived from sequence properties have been shown to have superior accuracy when compared to traditional approaches for the task of remote homology detection. Results: We introduce a new method for feature vector representation based on the physicochemical properties of the primary protein sequence. A distribution of physicochemical property scores are assembled from 4-mers of the sequence and normalized based on the null distribution of the property over all possible 4-mers. With this approach there is little computational cost associated with the transformation of the protein into feature space, and overall performance in terms of remote homology detection is comparable with current state-of-the-art methods. We demonstrate that the features can be used for the task of pairwise remote homology detection with improved accuracy versus sequence-based methods such as BLAST and other feature-based methods of similar computational cost. Conclusions: A protein feature method based on physicochemical properties is a viable approach for extracting features in a computationally inexpensive manner while retaining the sensitivity of SVM protein homology detection. Furthermore, identifying features that can be used for generic pairwise homology detection in lieu of family-based homology detection is important for applications such as large database searches and comparative genomics.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC05-76RL01830; AC06-76RL01830

OSTI ID:: 1626267

Journal Information:: BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: 1 Vol. 11; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (32)

Remote homolog detection using local sequence-structure correlations Hou, Yuna; Hsu, Wynne; Lee, Mong Li Proteins: Structure, Function, and Bioinformatics, Vol. 57, Issue 3 https://doi.org/10.1002/prot.20221	journal	August 2004
Identification of common molecular subsequences Smith, T. F.; Waterman, M. S. Journal of Molecular Biology, Vol. 147, Issue 1, p. 195-197 https://doi.org/10.1016/0022-2836(81)90087-5	journal	March 1981
Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties Yang, Yuchen; Tantoso, Erwin; Li, Kuo-Bin Journal of Theoretical Biology, Vol. 252, Issue 1 https://doi.org/10.1016/j.jtbi.2008.01.028	journal	May 2008
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/s0022-2836(05)80360-2	journal	October 1990
Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships Liao, Li; Noble, William Stafford Journal of Computational Biology, Vol. 10, Issue 6 https://doi.org/10.1089/106652703322756113	journal	December 2003
Remote homology detection: a motif based approach Ben-Hur, A.; Brutlag, D. Bioinformatics, Vol. 19, Issue Suppl 1 https://doi.org/10.1093/bioinformatics/btg1002	journal	July 2003
Efficient remote homology detection using local structure Hou, Y.; Hsu, W.; Lee, M. L. Bioinformatics, Vol. 19, Issue 17 https://doi.org/10.1093/bioinformatics/btg317	journal	November 2003
Protein homology detection using string alignment kernels Saigo, H.; Vert, J. -P.; Ueda, N. Bioinformatics, Vol. 20, Issue 11 https://doi.org/10.1093/bioinformatics/bth141	journal	February 2004
Motif-based protein ranking by network propagation Kuang, R.; Weston, J.; Noble, W. S. Bioinformatics, Vol. 21, Issue 19 https://doi.org/10.1093/bioinformatics/bti608	journal	August 2005
Profile-based direct kernels for remote homology detection and fold recognition Rangwala, H.; Karypis, G. Bioinformatics, Vol. 21, Issue 23 https://doi.org/10.1093/bioinformatics/bti687	journal	September 2005
Application of latent semantic analysis to protein remote homology detection Dong, Q. -w.; Wang, X. -l.; Lin, L. Bioinformatics, Vol. 22, Issue 3 https://doi.org/10.1093/bioinformatics/bti801	journal	November 2005
Remote homology detection based on oligomer distances Lingner, T.; Meinicke, P. Bioinformatics, Vol. 22, Issue 18 https://doi.org/10.1093/bioinformatics/btl376	journal	July 2006
SVM-HUSTLE--an iterative semi-supervised machine learning approach for pairwise protein remote homology detection Shah, A. R.; Oehmen, C. S.; Webb-Robertson, B. -J. Bioinformatics, Vol. 24, Issue 6 https://doi.org/10.1093/bioinformatics/btn028	journal	February 2008
Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection Damoulas, Theodoros; Girolami, Mark A. Bioinformatics, Vol. 24, Issue 10 https://doi.org/10.1093/bioinformatics/btn112	journal	March 2008
Augmented training of hidden Markov models to recognize remote homologs via simulated evolution Kumar, A.; Cowen, L. Bioinformatics, Vol. 25, Issue 13 https://doi.org/10.1093/bioinformatics/btp265	journal	April 2009
AAindex: amino acid index database, progress report 2008 Kawashima, S.; Pokarowski, P.; Pokarowska, M. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm998	journal	December 2007
Identifying remote protein homologs by network propagation Noble, William S.; Kuang, Rui; Leslie, Christina FEBS Journal, Vol. 272, Issue 20 https://doi.org/10.1111/j.1742-4658.2005.04947.x	journal	October 2005
The Spectrum Kernel: a String Kernel for svm Protein Classification Leslie, Christina; Eskin, Eleazar; Noble, William Stafford Proceedings of the Pacific Symposium, Biocomputing 2002 https://doi.org/10.1142/9789812799623_0053	conference	November 2011
Combining classifiers for improved classification of proteins from sequence or structure Melvin, Iain; Weston, Jason; Leslie, Christina S. BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-389	journal	January 2008
A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis Liu, Bin; Wang, Xiaolong; Lin, Lei BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-510	journal	December 2008
Measuring Global Credibility with Application to Local Sequence Alignment Webb-Robertson, Bobbie-Jo M.; McCue, Lee Ann; Lawrence, Charles E. PLoS Computational Biology, Vol. 4, Issue 5 https://doi.org/10.1371/journal.pcbi.1000077	journal	May 2008
Protein Ranking by Semi-Supervised Network Propagation Weston, Jason; Kuang, Rui; Leslie, Christina Columbia University https://doi.org/10.7916/d8xp73c4	text	January 2006
Peptide/protein structure analysis using the chemical shift index method: Upfield α-CH values reveal dynamic helices and αL sites Andersen, Niels H.; Cao, Bolong; Chen, Chinpan Biochemical and Biophysical Research Communications, Vol. 184, Issue 2 https://doi.org/10.1016/0006-291X(92)90691-D	journal	April 1992
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
SVM-BALSA: Remote homology detection based on Bayesian sequence alignment Webb-Robertson, Bobbie-Jo; Oehmen, Christopher; Matzke, Melissa Computational Biology and Chemistry, Vol. 29, Issue 6 https://doi.org/10.1016/j.compbiolchem.2005.09.006	journal	December 2005
A feature vector integration approach for a generalized support vector machine pairwise homology algorithm Webb-Robertson, Bobbie-Jo M.; Oehmen, Christopher S.; Shah, Anuj R. Computational Biology and Chemistry, Vol. 32, Issue 6 https://doi.org/10.1016/j.compbiolchem.2008.07.017	journal	December 2008
Mismatch string kernels for discriminative protein classification Leslie, C. S.; Eskin, E.; Cohen, A. Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bioinformatics/btg431	journal	January 2004
Fast model-based protein homology detection without alignment Hochreiter, S.; Heusel, M.; Obermayer, K. Bioinformatics, Vol. 23, Issue 14 https://doi.org/10.1093/bioinformatics/btm247	journal	May 2007
RANKPROP: a web server for protein remote homology detection Melvin, I.; Weston, J.; Leslie, C. Bioinformatics, Vol. 25, Issue 1 https://doi.org/10.1093/bioinformatics/btn567	journal	November 2008
SIMPRO: simple protein homology detection method by using indirect signals Jung, I.; Kim, D. Bioinformatics, Vol. 25, Issue 6 https://doi.org/10.1093/bioinformatics/btp048	journal	January 2009
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
Protein Ranking by Semi-Supervised Network Propagation Weston, Jason; Kuang, Rui; Leslie, Christina BMC Bioinformatics, Vol. 7, Issue S1 https://doi.org/10.1186/1471-2105-7-S1-S10	journal	March 2006

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Using Amino Acid Physicochemical Distance Transformation for Fast Protein Remote Homology Detection Liu, Bin; Wang, Xiaolong; Chen, Qingcai PLoS ONE, Vol. 7, Issue 9 https://doi.org/10.1371/journal.pone.0046633	journal	September 2012
An Ensemble Method for Predicting Subnuclear Localizations from Primary Protein Structures Han, Guo Sheng; Yu, Zu Guo; Anh, Vo PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0057225	journal	February 2013
A comprehensive review and comparison of different computational methods for protein remote homology detection Chen, Junjie; Guo, Mingyue; Wang, Xiaolong Briefings in Bioinformatics, Vol. 19, Issue 2 https://doi.org/10.1093/bib/bbw108	journal	November 2016
BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches Liu, Bin Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx165	journal	December 2017
Physico-Chemically Weighted Kernel for SVM Protein Classification Jiang, Hao; Ching, Wai Ki Applied Mechanics and Materials, Vol. 195-196 https://doi.org/10.4028/www.scientific.net/amm.195-196.385	journal	August 2012

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