Chaining Multiple-Alignment Blocks

Zheng Zhang, Balaji Raghavachari, Ross C. Hardison, Webb Miller

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


We derive a time-efficient method for building a multiple alignment consisting of a highestscoring 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 ε-globin genes.

Original languageEnglish (US)
Pages (from-to)217-226
Number of pages10
JournalJournal of Computational Biology
Issue number3
StatePublished - 1994

All Science Journal Classification (ASJC) codes

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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