STRIKE: evaluation of protein MSAs using a single 3D structure.
BACKGROUND
Evaluating alternative multiple protein sequence alignments is an important unsolved problem in Biology. The most accurate way of doing this is to use structural information. Unfortunately, most methods require at least two structures to be embedded in the alignment, a condition rarely met when dealing with standard datasets.


RESULTS
We developed STRIKE, a method that determines the relative accuracy of two alternative alignments of the same sequences using a single structure. We validated our methodology on three commonly used reference datasets (BAliBASE, Homestrad and Prefab). Given two alignments, STRIKE manages to identify the most accurate one in 70% of the cases on average. This figure increases to 79% when considering very challenging datasets like the RV11 category of BAliBASE. This discrimination capacity is significantly higher than that reported for other metrics such as Contact Accepted mutation or Blosum. We show that this increased performance results both from a refined definition of the contacts and from the use of an improved contact substitution score.


BACKGROUND
cedric.notredame@crg.eu


BACKGROUND
STRIKE is an open source freeware available from www.tcoffee.org


BACKGROUND
Supplementary data are available at Bioinformatics online.
Bioinformatics and Genomics Program, Centre for Genomic Regulation and UPF, Aiguader, 88, 08003 Barcelona, Spain.
Carsten
C
Kemena
Jean-Francois
JF
Taly
Jens
J
Kleinjung
Cedric
C
Notredame
D019295:Computational Biology / Q000379:methods; D020407:Internet; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
D011506:Proteins