UNIT 10.4 MultiPipMaker: Comparative Alignment Server for Multiple DNA Sequences

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

Published Online: 1 APR 2005

DOI: 10.1002/0471250953.bi1004s9

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Elnitski, L., Riemer, C., Burhans, R., Hardison, R. and Miller, W. 2005. MultiPipMaker: Comparative Alignment Server for Multiple DNA Sequences. Current Protocols in Bioinformatics. 9:10.4:10.4.1–10.4.12.

Author Information

  1. The Pennsylvania State University, University Park, Pennsylvania

Publication History

  1. Published Online: 1 APR 2005
  2. Published Print: MAR 2005

This is not the most recent version of the article. View current version (1 JUN 2010)


The MultiPipMaker World Wide Web server (http://www.bx.psu.edu) provides a useful tool for aligning multiple sequences and visualizing regions of conservation between them. This unit describes the use of the MultiPipMaker server 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 or stacked, pairwise percent identity plots, and user-specified annotations for genomic features and elements of choice, with clickable links to additional information. Alignments can include unordered, unoriented secondary sequences.


  • multiple alignment;
  • percent identity plots;
  • genomic analyses;
  • conserved noncoding sequences