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Bioinformatics Vol. 19 no. 9 2003
Pages 1155-1161
© 2003 Oxford University Press

RASCAL: rapid scanning and correction of multiple sequence alignments

J. D. Thompson , J. C. Thierry and O. Poch *

Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS/INSERM/ULP), B.P. 10142, 67404 Illkirch Cedex, France

Received on October 16, 2002 ; revised on December 16, 2002 ; accepted on January 13, 2003

Motivation: Most multiple sequence alignment programs use heuristics that sometimes introduce errors into the alignment. The most commonly used methods to correct these errors use iterative techniques to maximize an objective function. We present here an alternative, knowledge-based approach that combines a number of recently developed methods into a two-step refinement process. The alignment is divided horizontally and vertically to form a ‘lattice’ in which well aligned regions can be differentiated. Alignment correction is then restricted to the less reliable regions, leading to a more reliable and efficient refinement strategy

Results: The accuracy and reliability of RASCAL is demonstrated using: (i) alignments from the BAliBASE benchmark database, where significant improvements were often observed, with no deterioration of the existing high-quality regions, (ii) a large scale study involving 946 alignments from the ProDom protein domain database, where alignment quality was increased in 68% of the cases; and (iii) an automatic pipeline to obtain a high-quality alignment of 695 full-length nuclear receptor proteins, which took 11 min on a DEC Alpha 6100 computer

Availability: RASCAL is available at ftp://ftp-igbmc.u-strasbg.fr/pub/RASCAL

Contact: poch{at}igbmc.u-strasbg.fr

Supplementary information: http://bioinfo-igbmc.u-strasbourg.fr/BioInfo/RASCAL/paper/rascal_supp.html

* To whom correspondence should be addressed.


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