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Identifying common local segments, also called motifs, in multiple protein sequences plays an important role for establishing homology between proteins. Homology is easy to establish when sequences are similar (sharing an identity > 25%). However, for distant proteins, it is much more difficult to align motifs that are not similar in sequences but still share common structures or functions. This paper is a first attempt to align multiple protein sequences using both primary and secondarydoi:10.1089/cmb.2006.13.1735 pmid:17238842 fatcat:ncxydwkdhjcmtlksw6dpiyn5fm