publication . Other literature type . Article . 1994

CLUSTAL W: IMPROVING THE SENSITIVITY OF PROGRESSIVE MULTIPLE SEQUENCE ALIGNMENT THROUGH SEQUENCE WEIGHTING, POSITION-SPECIFIC GAP PENALTIES AND WEIGHT MATRIX CHOICE

Julie D. Thompson; Desmond G. Higgins; Toby J. Gibson;
Open Access
  • Published: 11 Nov 1994
  • Publisher: Springer Netherlands
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 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, posi...
Subjects
free text keywords: Gap penalty, Genetics, Multiple sequence alignment, Alignment-free sequence analysis, Biology, Sequence logo, Structural alignment, MUSCLE, BLOSUM, Substitution matrix
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