Advanced PipMaker (instructions) aligns two DNA sequences and returns a percent identity plot of that alignment, together with a traditional textual form of the alignment.

Pick one: Search both strands Search one strand
Pick one: Show all matches Chaining Single coverage
Select: High sensitivity and low time limit

Select output:
PIP (optional title: )
Dotplot form of the alignments
Concise textual form of the alignments
Traditional textual form of the alignments (very verbose; may exceed your mail quota; you do not want this)
Analysis of exons (requires exons file)
Raw blastz output (for Laj or SGP-1)
Order and orient contigs (returns a text file, a dotplot, and the reordered sequence) [Split second sequence into contigs on NN...]

Generate: PostScript PDF PDF with embedded contig names

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Development and maintenance of PipMaker is supported by grant HG02238 from the National Human Genome Research Institute.

If you publish results obtained using PipMaker, please cite Schwartz et al., Genome Research 10:577-586, April 2000.