Having shown how to make alignments using VISTA, we will now show how to make a PipMaker alignment using the same sequences as for VISTA. Browse for your saved mouse sequence file under first sequence filename; browse for your saved human sequence under second sequence filename. Enter your e-mail address.

Browse for the mouse repeats file from VISTA under first sequence mask. If you have not run VISTA, use RepeatMasker to generate the first sequence mask. Browse for the mouse annotation file under first sequence exons.

We will not use the last three optional files (first sequence underlay, annotations, and user supplied alignment). Users interested in these options should consult PipMaker Advanced Instructions.

Choose the options to search both strands and show all matches.

Check the output options that are shown. If your e-mail system does not handle big files, omit the traditional textual form. Choose the PDF option for the output format. Also, choose to receive the results by e-mail; PipMaker will not process large files over the web.

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.

• First sequence filename (FASTA format) (file must be plain text only):
  
  
• Second sequence filename (FASTA format) (file must be plain text only):
  
  
• Your email address:
  
  
• Optional features:
  
  • First sequence mask:
    
    
  • First sequence exons:
    
    
  • First sequence underlay:
    
    
  • Annotations:
    
    
  • User supplied 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

Get results via: email www

Email the authors at: <pipmaster@bio.cse.psu.edu>

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.