PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a “percent identity plot”, or “pip” for short.
MultiPipMaker allows the user to see relationships among more than two sequences. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics
- C COmpiler
:: MORE INFORMATION
Schwartz et al.,
PipMakerA Web Server for Aligning Two Genomic DNA Sequences
Genome Research 10:577-586, April 2000.
MultiPipMaker: a comparative alignment server for multiple DNA sequences.
Elnitski L, Burhans R, Riemer C, Hardison R, Miller W.
Curr Protoc Bioinformatics. 2010 Jun;Chapter 10:Unit10.4. doi: 10.1002/0471250953.bi1004s30.