MultiPipMaker: comparative alignment server for multiple DNA sequences.

The MultiPipMaker World Wide Web server (http://www.bx.psu.edu) provides a useful tool for aligning multiple sequences and visualizing regions of conservation between them. This unit describes the use of the MultiPipMaker server and gives an explanation of the resulting output files and supporting tools. Features provided by the server include alignment of up to 20 very long genomic sequences, output choices of a true, nucleotide-level multiple alignment or stacked, pairwise percent identity plots, and user-specified annotations for genomic features and elements of choice, with clickable links to additional information. Alignments can include unordered, unoriented secondary sequences.