UNIT 10.2 PipMaker: A World Wide Web Server for Genomic Sequence Alignments
Published Online: 1 FEB 2003
Copyright © 2003 by John Wiley and Sons, Inc.
Lab Protocol Title
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.
- Published Online: 1 FEB 2003
- 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.