DbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches

Abstract

DbClustal addresses the important problem of the automatic multiple alignment of the top scoring full-length sequences detected by a database homology search. By combining the advantages of both local and global alignment algorithms into a single system, DbClustal is able to provide accurate global alignments of highly divergent, complex sequence sets. Local alignment information is incorporated into a ClustalW global alignment in the form of a list of anchor points between pairs of sequences. The method is demonstrated using anchors supplied by the Blast post-processing program, Ballast. The rapidity and reliability of DbClustal have been demonstrated using the recently annotated Pyrococcus abyssi proteome where the number of alignments with totally misaligned sequences was reduced from 20% to <2%. A web site has been implemented proposing BlastP database searches with automatic alignment of the top hits by DbClustal.