Format

Send to

Choose Destination
Bioinformatics. 2011 Dec 15;27(24):3385-91. doi: 10.1093/bioinformatics/btr587. Epub 2011 Oct 28.

STRIKE: evaluation of protein MSAs using a single 3D structure.

Author information

1
Bioinformatics and Genomics Program, Centre for Genomic Regulation and UPF, Aiguader, 88, 08003 Barcelona, Spain.

Abstract

MOTIVATION:

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.

RESULT:

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.

CONTACT:

cedric.notredame@crg.eu

AVAILABILITY:

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

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22039207
PMCID:
PMC3232373
DOI:
10.1093/bioinformatics/btr587
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center