MultiPipMaker: A comparative alignment server for multiple DNA sequences

Laura Elnitski, Richard Burhans, Cathy Riemer, Ross Hardison, Webb Miller

Research output: Contribution to journalReview articlepeer-review

8 Scopus citations


The MultiPipMaker World Wide Web server ( provides a tool for aligning multiple DNA sequences and visualizing regions of conservation among them. This unit describes its use and gives an explanation of the resulting output files and supporting tools. Features provided by the server include alignment of up to 20 very long genomic sequences, output choices of a true, nucleotide-level multiple alignment and/or stacked, pairwise percent identity plots, and support for user-specified annotations of genomic features and arbitrary regions, with clickable links to additional information. Input sequences other than the reference can be fragmented, unordered, and unoriented.

Original languageEnglish (US)
Pages (from-to)10.4.1-10.4.14
JournalCurrent Protocols in Bioinformatics
Issue numberSUPPL. 30
StatePublished - Jun 2010

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry


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