title: PipMaker: a World Wide Web server for genomic sequence alignments.
abstract: 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.
authors.affiliation: The Pennsylvania State University, University Park, Pennsylvania, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Elnitski
authors.forename: Cathy
authors.initials: C
authors.lastname: Riemer
authors.forename: Scott
authors.initials: S
authors.lastname: Schwartz
authors.forename: Ross
authors.initials: R
authors.lastname: Hardison
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D002874:Chromosome Mapping / Q000379:methods*; D020407:Internet; D010363:Pattern Recognition, Automated / Q000379:methods; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software