PipMaker: a World Wide Web server for genomic sequence alignments.

Laura Elnitski, Cathy Riemer, Scott Schwartz, Ross Cameron Hardison, Webb Miller

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


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.

Original languageEnglish (US)
JournalCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
VolumeChapter 10
StatePublished - Jan 1 2003

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry


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