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Quantification of the variation in percentage identity for protein sequence alignments.

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title Quantification of the variation in percentage identity for protein sequence alignments.
 
Creator Raghava, G.P.S.
Barton, Geoffrey J
 
Subject QR Microbiology
 
Description Although it is well known amongst expert sequence analysts that PID is a poor score for discriminating between protein sequences, the apparent simplicity of the percentage identity score encourages its widespread use in establishing cutoffs for structural similarity. This paper illustrates that not only is PID a poor measure of sequence similarity when compared to the Z-score, but that there is also a large uncertainty in reported PID values. Since better alternatives to PID exist to quantify sequence similarity, these should be quoted where possible in preference to PID. The findings presented here should prove helpful to those new to sequence analysis, and in warning those who seek to interpret the value of a PID reported in the literature.
 
Publisher Biomedcentral
 
Date 2006
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://crdd.osdd.net/open/67/1/raghava2006.4.pdf
Raghava, G.P.S. and Barton, Geoffrey J (2006) Quantification of the variation in percentage identity for protein sequence alignments. BMC bioinformatics, 7. p. 415. ISSN 1471-2105
 
Relation http://www.biomedcentral.com/content/pdf/1471-2105-7-415.pdf
http://crdd.osdd.net/open/67/