TITLE

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments

AUTHOR(S)
O. O'Sullivan; M. Zehnder; D. Higgins; P. Bucher; A. Grosdidier; C. Notredame
PUB. DATE
January 2009
SOURCE
Bioinformatics;Jan2009 Supplement, Vol. 19, p215
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods. Results: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages. Availability: APDB is implemented in C, its source code and its documentation are available for free on request from the authors. Contact: cedric.notredame@europe.com
ACCESSION #
11047054

 

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