A SIMPLE METHOD TO GENERATE NONTRIVIAL ALTERNATE ALIGNMENTS OF PROTEIN SEQUENCES

被引:38
作者
SAQI, MAS
STERNBERG, MJE
机构
[1] Biomolecular Modelling Laboratory Imperial Cancer Research Fund PO Box 123
关键词
SEQUENCE ALIGNMENT; DYNAMIC PROGRAMMING; SUBOPTIMAL PATHS; PROTEIN STRUCTURE PREDICTION; HOMOLOGY MODELING;
D O I
10.1016/0022-2836(91)90667-U
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A major problem in sequence alignments based on the standard dynamic programming method is that the optimal path does not necessarily yield the best equivalencing of residues assessed by structural or functional criteria. An algorithm is presented that finds suboptimal alignments of protein sequences by a simple modification to the standard dynamic programming method. The standard pairwise weight matrix elements are modified in order to penalize, but not eliminate, the equivalencing of residues obtained from previous alignments. The algorithm thereby yields a limited set of alternate alignments that can differ considerably from the optimal. The approach is benchmarked on the alignments of immunoglobulin domains. Without a prior knowledge of the optimal choice of gap penalty, one of the suboptimal alignments is shown to be more accurate than the optimal. © 1991.
引用
收藏
页码:727 / 732
页数:6
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