Computational Biology

A sensitive method for multiple sequence alignment should be able to align local motifs that are contained in some but not necessarily in all of the input sequences. In addition, it should be possible to integrate various of such partial local alignments into one single multiple output alignment. This leads to the question of consistency of partial alignments. Based on a new set-theoretical definition of sequence alignment, the consistency problem is discussed theoretically, and a recently developed library of C functions for consistency calculation (GABIOSLIB) is described. GABIOS-LIB has been integrated into the DIALIGN alignment program to carry out consistency tests during the multiple alignment procedure. While the resulting alignments are exactly the same as with the previous version of DIALIGN, the running time of the program has been crucially improved. For large data sets, the new version of DIALIGN is up to 120 times faster than the old version. Availability: http://bibiserv.TechFak.Uni-Bielefeld.DE/dialign/

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