UNIT 10.2 PipMaker: A World Wide Web Server for Genomic Sequence Alignments

  1. Laura Elnitski,
  2. Cathy Riemer,
  3. Scott Schwartz,
  4. Ross Hardison,
  5. Webb Miller

Published Online: 1 FEB 2003

DOI: 10.1002/0471250953.bi1002s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Elnitski, L., Riemer, C., Schwartz, S., Hardison, R. and Miller, W. 2003. PipMaker: A World Wide Web Server for Genomic Sequence Alignments. Current Protocols in Bioinformatics. 00:10.2:10.2.1–10.2.23.

Author Information

  1. The Pennsylvania State University, University Park, Pennsylvania

Publication History

  1. Published Online: 1 FEB 2003
  2. Published Print: JAN 2003


PipMaker is a World-Wide Web site used to compare two long genomic sequences and identify conserved segments between them. This unit describes the use of the PipMaker server and explains the resulting output files. PipMaker provides an efficient method of aligning genomic sequences and returns a compact, but easy-to-interpret form of output, the percent identity plot (pip). For each aligning segment between two sequences the pip shows both the position relative to the first sequence and the degree of similarity. Optional annotations on the pip provide additional information to assist in the interpretation of the alignment. The default parameters of the underlying blastz alignment program are tuned for human-mouse alignments.