Software tools for analyzing pairwise alignments of long sequences

Scott Schwartz, Webb Miller, Cher ming Yang, Ross C. Hardison

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


Pairwise comparison of long stretches of genomic DNA sequence can Identify regions conserved across species, which often indicate functional significance. However, the novel insights frequently must be winnowed from a flood of information; for instance, running an alignment program on two 50-kilobase sequences might yield over a hundred pages of alignments. Direct inspection of such a volume of printed output Is infeasible, or at best highly undesirable, and computer tools are needed to summarize the information, to assist in its analysis, and to report the findings. This paper describes two such software tools. One tool prepares publication-quality pictorial representations of alignments, while another facilitates interactive browsing of pairwise alignment data. Their effectiveness is illustrated by comparing the β-like globin gene clusters between humans and rabbits. A second example compares the chioroplast genomes of tobacco and liverwort.

Original languageEnglish (US)
Pages (from-to)4663-4667
Number of pages5
JournalNucleic acids research
Issue number17
StatePublished - Sep 11 1991

All Science Journal Classification (ASJC) codes

  • Genetics


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