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

Authors
  • Raghava, G P S
  • Barton, Geoffrey J
Type
Published Article
Journal
BMC Bioinformatics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Jan 01, 2006
Volume
7
Pages
415–415
Identifiers
PMID: 16984632
Source
Medline
License
Unknown

Abstract

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.

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