Revisiting Amino Acid Substitution Matrices for Identifying Distantly Related Proteins

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2013 Nov 28

PMID 24281694

Citations 28

Authors

Kazunori Yamada

Kentaro Tomii

Affiliations

Soon will be listed here.

Abstract

Motivation: Although many amino acid substitution matrices have been developed, it has not been well understood which is the best for similarity searches, especially for remote homology detection. Therefore, we collected information related to existing matrices, condensed it and derived a novel matrix that can detect more remote homology than ever.

Results: Using principal component analysis with existing matrices and benchmarks, we developed a novel matrix, which we designate as MIQS. The detection performance of MIQS is validated and compared with that of existing general purpose matrices using SSEARCH with optimized gap penalties for each matrix. Results show that MIQS is able to detect more remote homology than the existing matrices on an independent dataset. In addition, the performance of our developed matrix was superior to that of CS-BLAST, which was a novel similarity search method with no amino acid matrix. We also evaluated the alignment quality of matrices and methods, which revealed that MIQS shows higher alignment sensitivity than that with the existing matrix series and CS-BLAST. Fundamentally, these results are expected to constitute good proof of the availability and/or importance of amino acid matrices in sequence analysis. Moreover, with our developed matrix, sophisticated similarity search methods such as sequence-profile and profile-profile comparison methods can be improved further.

Availability And Implementation: Newly developed matrices and datasets used for this study are available at http://csas.cbrc.jp/Ssearch/.

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References

Jung J, Lee B . Use of residue pairs in protein sequence-sequence and sequence-structure alignments. Protein Sci. 2000; 9(8):1576-88. PMC: 2144723. DOI: 10.1110/ps.9.8.1576. View

Liu X, Zhao Y . Substitution matrices of residue triplets derived from protein blocks. J Comput Biol. 2010; 17(12):1679-87. DOI: 10.1089/cmb.2008.0035. View

Gambin A, Lasota S, Szklarczyk R, Tiuryn J, Tyszkiewicz J . Contextual alignment of biological sequences (Extended abstract). Bioinformatics. 2002; 18 Suppl 2:S116-27. DOI: 10.1093/bioinformatics/18.suppl_2.s116. View

Hourai Y, Akutsu T, Akiyama Y . Optimizing substitution matrices by separating score distributions. Bioinformatics. 2004; 20(6):863-73. DOI: 10.1093/bioinformatics/btg494. View

Dimmic M, Rest J, Mindell D, Goldstein R . rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J Mol Evol. 2002; 55(1):65-73. DOI: 10.1007/s00239-001-2304-y. View

Lewis T, Sillitoe I, Andreeva A, Blundell T, Buchan D, Chothia C . Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res. 2012; 41(Database issue):D499-507. PMC: 3531217. DOI: 10.1093/nar/gks1266. View

Crooks G, Green R, Brenner S . Pairwise alignment incorporating dipeptide covariation. Bioinformatics. 2005; 21(19):3704-10. DOI: 10.1093/bioinformatics/bti616. View

Biegert A, Soding J . Sequence context-specific profiles for homology searching. Proc Natl Acad Sci U S A. 2009; 106(10):3770-5. PMC: 2645910. DOI: 10.1073/pnas.0810767106. View

Sillitoe I, Cuff A, Dessailly B, Dawson N, Furnham N, Lee D . New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res. 2012; 41(Database issue):D490-8. PMC: 3531114. DOI: 10.1093/nar/gks1211. View

10.

Gough J, Karplus K, Hughey R, Chothia C . Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 2001; 313(4):903-19. DOI: 10.1006/jmbi.2001.5080. View

11.

Lee M, Chan M, Bundschuh R . Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches. Bioinformatics. 2008; 24(11):1339-43. DOI: 10.1093/bioinformatics/btn130. View

12.

Benner S, Cohen M, Gonnet G . Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng. 1994; 7(11):1323-32. DOI: 10.1093/protein/7.11.1323. View

13.

Gribskov M, Robinson N . Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput Chem. 1996; 20(1):25-33. DOI: 10.1016/s0097-8485(96)80004-0. View

14.

Jimenez-Morales D, Liang J . Pattern of amino acid substitutions in transmembrane domains of β-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria. PLoS One. 2011; 6(11):e26400. PMC: 3206045. DOI: 10.1371/journal.pone.0026400. View

15.

Kann M, Qian B, Goldstein R . Optimization of a new score function for the detection of remote homologs. Proteins. 2000; 41(4):498-503. DOI: 10.1002/1097-0134(20001201)41:4<498::aid-prot70>3.0.co;2-3. View

16.

Vingron M, Waterman M . Sequence alignment and penalty choice. Review of concepts, case studies and implications. J Mol Biol. 1994; 235(1):1-12. DOI: 10.1016/s0022-2836(05)80006-3. View

17.

Fu L, Niu B, Zhu Z, Wu S, Li W . CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2. PMC: 3516142. DOI: 10.1093/bioinformatics/bts565. View

18.

Henikoff S, Henikoff J . Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992; 89(22):10915-9. PMC: 50453. DOI: 10.1073/pnas.89.22.10915. View

19.

Ng P, Henikoff J, Henikoff S . PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics. 2000; 16(9):760-6. DOI: 10.1093/bioinformatics/16.9.760. View

20.

Brick K, Pizzi E . A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins. BMC Bioinformatics. 2008; 9:236. PMC: 2408606. DOI: 10.1186/1471-2105-9-236. View