MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences

Scott Schwartz, Laura Elnitski, Mei Li, Matt Weirauch, Cathy Riemer, Arian Smit, Jim Thomas, Jeff Touchman, Bob Blakesley, Gerry Bouffard, Steve Beckstrom-Sternberg, Pam Thomas, Jenny McDowell, Baishali Maskeri, Nancy Hansen, Elliott Margulies, Eric D. Green, Ross C. Hardison, Webb Miller

Research output: Contribution to journalArticlepeer-review

192 Scopus citations


Analysis of multiple sequence alignments can generate important, testable hypotheses about the phylogenetic history and cellular function of genomic sequences. We describe the MultiPipMaker server, which aligns multiple, long genomic DNA sequences quickly and with good sensitivity (available at since May 2001). Alignments are computed between a contiguous reference sequence and one or more secondary sequences, which can be finished or draft sequence. The outputs include a stacked set of percent identity plots, called a MultiPip, comparing the reference sequence with subsequent sequences, and a nucleotide-level multiple alignment. New tools are provided to search MultiPipMaker output for conserved matches to a user-specified pattern and for conserved matches to position weight matrices that describe transcription factor binding sites (singly and in clusters). We illustrate the use of MultiPipMaker to identify candidate regulatory regions in WNT2 and then demonstrate by transfection assays that they are functional. Analysis of the alignments also confirms the phylogenetic inference that horses are more closely related to cats than to cows.

Original languageEnglish (US)
Pages (from-to)3518-3524
Number of pages7
JournalNucleic acids research
Issue number13
StatePublished - Jul 1 2003

All Science Journal Classification (ASJC) codes

  • Genetics


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