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Aligning protein sequence and analysing substitution pattern using a class-specific matrix

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Abstract

Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological research. However, alignment in the ‘twilight zone’ remains an open issue. It is feasible and necessary to construct a new score matrix as more protein structures are resolved. Three structural class-specific score matrices (all-alpha, allbeta and alpha/beta) were constructed based on the structure alignment of low identity proteins of the corresponding structural classes. The class-specific score matrices were significantly better than a structure-derived matrix (HSDM) and three other generalized matrices (BLOSUM30, BLOSUM60 and Gonnet250) in alignment performance tests. The optimized gap penalties presented here also promote alignment performance. The results indicate that different protein classes have distinct amino acid substitution patterns, and an amino acid score matrix should be constructed based on different structural classes. The class-specific score matrices could also be used in profile construction to improve homology detection.

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Abbreviations

DSSP:

Database of Secondary Structure assignment Program

GEP:

gap extension penalty

GOP:

gap opening penalty

HMM:

hidden Markov model

PD:

pattern distance

SCOP:

structural classification of proteins

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Authors and Affiliations

  1. College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China

    Hai Song Xu, Wen Ke Ren, Xiao Hui Liu & Xiao Qin Li

Authors
  1. Hai Song Xu
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  2. Wen Ke Ren
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  3. Xiao Hui Liu
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  4. Xiao Qin Li
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Corresponding author

Correspondence to Xiao Qin Li.

Additional information

Authors’ contributions: XQL and XHL did some preliminary work on sequence data collection and classification. WKR participated in part of the programming work. HSX conducted most of the programming work, the statistical analysis and result analysis. HSX drafted the manuscript. The whole work was conceived by HSX, WKR, XHL and XQL and was supervised by XQL. All the authors read and approved of the final manuscript.

Supplementary tables and figures pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/June2010/pp295-314/suppl.pdf

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Xu, H.S., Ren, W.K., Liu, X.H. et al. Aligning protein sequence and analysing substitution pattern using a class-specific matrix. J Biosci 35, 295–314 (2010). https://doi.org/10.1007/s12038-010-0033-3

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  • DOI: https://doi.org/10.1007/s12038-010-0033-3

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