Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set

Motivation: SAM-T99 is an iterative hidden Markov model-based method for fi nding proteins similar to a single target sequence and aligning them. One o f its main uses is to produce multiple alignments of homologs of the target sequence. Previous tests of SAM-T99 and its predecessors have concentrated on the quality of the searches performed, not on the quality of the multip le alignment. In this paper we report on tests of multiple alignment qualit y, comparing SAM-T99 to the standard multiple aligner, CLUSTALW. Results: The paper evaluates the multiple-alignment aspect of the SAM-T99 p rotocol, using the BAliBASE benchmark alignment database. On these benchmar ks, SAM-T99 is comparable in accuracy with ClustalW.