Chaining multiple-alignment blocks.
We derive a time-efficient method for building a multiple alignment consisting of a highest-scoring chain of "blocks," i.e., short gap-free alignments. Besides executing faster than a general-purpose multiple-alignment program, the method may be particularly appropriate when discovery of blocks meeting a certain criterion is the main reason for aligning the sequences. Utility of the method is illustrated by locating a chain of "phylogenetic footprints" (specifically, exact matches of length 6 or more) in the 5'-flanking regions of six mammalian epsilon-globin genes.
Zhang
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Z
Department of Computer Science and Engineering, Pennsylvania State University, University Park 16802, USA.
Raghavachari
B
B
Hardison
R C
RC
Miller
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W
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D005914:Globins / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*
D005914:Globins