creators_name: Raghava, G.P.S.
creators_name: Barton, Geoffrey J
type: article
datestamp: 2012-01-10 08:06:05
lastmod: 2012-01-10 08:06:05
metadata_visibility: show
title: Quantification of the variation in percentage identity for protein sequence alignments.
ispublished: pub
subjects: QR
full_text_status: public
note: OPEN ACCESS
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.
date: 2006
date_type: published
publication: BMC bioinformatics
volume: 7
publisher: Biomedcentral
pagerange: 415
refereed: TRUE
issn: 1471-2105
official_url: http://www.biomedcentral.com/content/pdf/1471-2105-7-415.pdf
related_url_type: pub
citation:   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     
document_url: http://crdd.osdd.net/open/67/1/raghava2006.4.pdf