Comparative analysis of multiple protein-sequence alignment methods [published erratum appears in Mol Biol Evol 1994 Sep;11(5):811]

We have analyzed a total of 12 different global and local multipleprotein-sequence alignment methods. The purpose of this study is toevaluate each method's ability to correctly identify the ordered series ofmotifs found among all members of a given protein family. Fourphylogenetically distributed sets of sequences from the hemoglobin, kinase,aspartic acid protease, and ribonuclease H protein families were used totest the methods. The performance of all 12 methods was affected by (1) thenumber of sequences in the test sets, (2) the degree of similarity amongthe sequences, and (3) the number of indels required to produce a multiplealignment. Global methods generally performed better than local methods inthe detection of motif patterns.