UNIT 10.4 MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences

  1. Laura Elnitski,
  2. Richard Burhans,
  3. Cathy Riemer,
  4. Ross Hardison,
  5. Webb Miller

Published Online: 1 JUN 2010

DOI: 10.1002/0471250953.bi1004s30

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Elnitski, L., Burhans, R., Riemer, C., Hardison, R. and Miller, W. 2010. MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences. Current Protocols in Bioinformatics. 30:10.4:10.4.1–10.4.14.

Author Information

  1. The Pennsylvania State University, University Park, Pennsylvania

Publication History

  1. Published Online: 1 JUN 2010
  2. Published Print: JUN 2010


The MultiPipMaker World Wide Web server (http://www.bx.psu.edu) 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. Curr. Protoc. Bioinform. 30:10.4.1-10.4.14. © 2010 by John Wiley & Sons, Inc.


  • multiple alignment;
  • percent identity plot;
  • genomic analysis;
  • conserved non-coding sequences