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Most Cited Journal Articles 2005-Chemistry and Related

Following is a CAS database record representing a highly cited journal article.

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CAS subject entries for this document include: Protein sequences; Computer program .

CAPLUS COPYRIGHT 2006 ACS on STN

TITLE:	CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
AUTHOR(S):	Thompson, Julie D.; Higgins, Desmond G.; Gibson, Toby J.
CORPORATE SOURCE:	European Molecular Biology laboratory, Heidelberg, D-69012, Germany
SOURCE:	Nucleic Acids Research (1994), 22(22), 4673-80 CODEN: NARHAD; ISSN: 0305-1048
PUBLISHER:	Oxford University Press
LANGUAGE:	English

ABSTRACT:
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual wts. are assigned to each sequence in a partial alignment in order to down-wt. near-duplicate sequences and up-wt. the most divergent ones. Secondly, amino acid substitution matrixes 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 of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.