MIX-N-MATCH - AN IMPROVED MULTIPLE SEQUENCE ALIGNMENT PROCEDURE FOR DISTANTLY RELATED PROTEINS USING SECONDARY STRUCTURE PREDICTIONS, DESIGNED TO BE INDEPENDENT OF THE CHOICE OF GAP PENALTY AND SCORING MATRIX
Lh. Bell et al., MIX-N-MATCH - AN IMPROVED MULTIPLE SEQUENCE ALIGNMENT PROCEDURE FOR DISTANTLY RELATED PROTEINS USING SECONDARY STRUCTURE PREDICTIONS, DESIGNED TO BE INDEPENDENT OF THE CHOICE OF GAP PENALTY AND SCORING MATRIX, Protein engineering, 6(7), 1993, pp. 683-690
A new multiple sequence alignment procedure is presented. Several diff
erent multiple alignments are made using differing criteria. Having di
vided the sequences into strongly conserved regions (SCRs) and loosely
conserved regions (LCRs), the 'best' alignment for each LCR is chosen
, independently of the other LCRs, from a selection of possibilities i
n the multiple alignments. To help make this choice for each LCR, the
secondary structure is predicted and shown alongside each different po
ssible alignment. One advantage of this method over automatic, non-int
eractive methods, is that the final alignment is not dependent on the
choice of a single set of scoring parameters. Another is that, by allo
wing interactive choice and by taking account of secondary structural
information, the final alignment is based more on biological rather th
an mathematical factors. This method can produce better alignments tha
n any of the initial automatic multiple alignment methods used.