nodalpoint.org - Clarifying simple things that end up complicated: Percentage Identity - Comments

Z-scores eek....

emelamud — Fri, 29 Sep 2006 11:59:47 -0400

There is more than one way of calculating Z-score as well, and distribution of randomized alignment values is not perfectly normal, so the question if Z-score is right measure to begin with. Don't get me wrong, PID calculations have their problems as well, local vs global alignment, definition of overlap region etc. PID values have a nice intuitive feel for any biologist, the same can't be said about Z-score.

new journal needed

Neil — Fri, 29 Sep 2006 01:10:10 -0400

There should be a new journal for this sort of thing: "Journal of non-earth shattering results", perhaps. On the other hand, authors worried about their output can gain some comfort (and start writing up some of their more obvious findings).

Remember Katoh?

Animesh — Thu, 28 Sep 2006 05:02:10 -0400

I will remind you of the Katoh [ http://www.nodalpoint.org/2006/04/07/how_to_get_many_pubmed_entries_when... ]post.
By the way guys, did you read Dilbert's blog [ http://dilbertblog.typepad.com/the_dilbert_blog/2006/09/answer_to_the_p...., ]? Moist robots... are we? May be worse...

______________________"The Answer Lies in Genome"______________________
http://sharma.animesh.googlepages.com/

Clarifying simple things that end up complicated: Percentage Identity

pansapiens — Fri, 22 Sep 2006 23:03:56 -0400

A new paper by Raghava and Barton has just gone online "Quantification of the variation in percentage identity for protein sequence alignments" at BMC Bioinformatics.

Initially I was shocked .. how, in 2006, could anyone manage to publish anything original about percentage identity (PID), that simple but oft used/abused measure that is fundamental in the definition of the "twilight-zone" of sequence similarity (for infering structural similarity or relatedness by sequence alone).

Well, it turns out (and becomes obvious when you try to code it), that there is more than one way to calculate the PID of a multiple sequence alignment, and each method yields different results. Authors rarely state exactly which method they used and, not surprisingly, no matter how you chose to measure the PID the multiple alignment algorithm used also has a substantial impact.