title: Chaining multiple-alignment blocks.
abstract: 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.
authors.affiliation: Department of Computer Science and Engineering, Pennsylvania State University, University Park 16802, USA.
authors.forename: Z
authors.initials: Z
authors.lastname: Zhang
authors.forename: B
authors.initials: B
authors.lastname: Raghavachari
authors.forename: R C
authors.initials: RC
authors.lastname: Hardison
authors.forename: W
authors.initials: W
authors.lastname: Miller
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D005914:Globins / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D005914:Globins