Thu, 21 Aug 2008 14:42:17 BST CiteULike: miguel's clustalw http://www.citeulike.org/user/miguel/tag/clustalw CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/miguel/article/94348 <i>Nucleic Acids Res, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680.</i><br /><br />The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson doi:10.1093/nar/22.22.4673 Nucleic Acids Res, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680. 2005-02-14T12:22:21-00:00 1994 Nucleic Acids Res 0305-1048 22 22 4673 4680 alignment clustalw