Stephen F Altschul, National Center for Biotechnology Information, Bethesda, Maryland, USA
Published online: March 2008
DOI: 10.1002/9780470015902.a0005265.pub2
A substitution matrix is a collection of scores for aligning nucleotides or amino acids with one another. These scores generally represent the relative ease with which one nucleotide or amino acid may mutate into or substitute for another, and they are used to measure similarity in sequence alignments.
Keywords: alignment score; sequence similarity; gap costs; PAM matrices; BLOSUM matrices
| References | |
| Altschul SF (1991) Amino acid substitution matrices from an information theoretic perspective. Journal of Molecular Biology 219: 555–565. | |
| Altschul SF, Wootton JC, Gertz EM et al. (2005) Protein database searches using compositionally adjusted substitution matrices. The FEBS Journal 272: 5101–5109. | |
| book Dayhoff MO, Schwartz RM and Orcutt BC (1978) "A model of evolutionary change in proteins". In: Dayhoff MO (ed.) Atlas of Protein Sequence and Structure, vol. 5 (suppl. 3), pp. 345–352. Washington, DC: National Biomedical Research Foundation. | |
| Henikoff S and Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences of the USA 89: 10915–10919. | |
| Henikoff S and Henikoff JG (1993) Performance evaluation of amino acid substitution matrices. Proteins 17: 49–61. | |
| Jones DT, Taylor WR and Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275–282. | |
| Karlin S and Altschul SF (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proceedings of the National Academy of Sciences of the USA 87: 2264–2268. | |
| Muller T, Rahmann S and Rehmsmeier M (2001) Non-symmetric score matrices and the detection of homologous transmembrane proteins. Bioinformatics 7(suppl. 1): S182–S189. | |
| Muller T and Vingron M (2000) Modeling amino acid replacement. Journal of Computational Biology 7: 761–776. | |
| Ng PC, Henikoff JG and Henikoff S (2000) PHAT: a transmembrane- specific substitution matrix. Bioinformatics 16: 760–766. | |
| Pearson WR (1995) Comparison of methods for searching protein sequence databases. Protein Science 4: 1145–1160. | |
| book Schwartz RM and Dayhoff MO (1978) "Matrices for detecting distant relationships". In: Dayhoff MO (ed.) Atlas of Protein Sequence and Structure, vol. 5 (suppl. 3), pp. 353–358. Washington, DC: National Biomedical Research Foundation. | |
| States DJ, Gish W and Altschul SF (1991) Improved sensitivity of nucleic acid database searches using application-specific scoring matrices. Methods 3: 66–70. | |
| Wan H and Wootton JC (2000) A global compositional complexity measure for biological sequences: AT-rich and GC-rich genomes encode less complex proteins. Computers and Chemistry 24: 71–94. | |
| Yu Y-K, Wootton JC and Altschul SF (2003) The compositional adjustment of amino acid substitution matrices. Proceedings of the National Academy of Sciences of the USA 100: 15688–15693. | |
| Further Reading | |
| Altschul SF (1993) A protein alignment scoring system sensitive at all evolutionary distances. Journal of Molecular Evolution 36: 290–300. | |
| book Chiaromonte F, Yap VB and Miller W (2002) "Scoring pairwise genomic sequence alignments". In: Altman RB, Dunker AK, Hunter L, Lauderdale K and Klein TE (eds) Pacific Symposium on Biocomputing, pp. 115–126. Singapore: World Scientific Publishing. | |
| Claverie J-M (1993) Detecting frameshifts by amino acid sequence comparison. Journal of Molecular Biology 234: 1140–1157. | |
| Dembo A, Karlin S and Zeitouni O (1994) Limit distribution of maximal non-aligned two-sequence segmental score. Annals of Probability 22: 2022–2039. | |
| book Durbin R, Eddy S, Krogh A and Mitchison G (1998) Biological Sequence Analysis. Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge University Press. | |
| book Ewens WJ and Grant GR (2001) Statistical Methods in Bioinformatics. New York, NY: Springer. | |
| Gonnet GH, Cohen MA and Benner SA (1992) Exhaustive matching of the entire protein sequence database. Science 256: 1443–1445. | |
| Henikoff S and Henikoff JG (2000) Amino acid substitution matrices. Advances in Protein Chemistry 54: 73–97. | |
| Vingron M and Waterman MS (1994) Sequence alignment and penalty choice. Review of concepts, case studies and implications. Journal of Molecular Biology 235: 1–12. | |
| Yu Y-K and Altschul SF (2005) The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. Bioinformatics 21: 902–911. | |
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