CrossMatcher: A Sequence Comparison Program for the Mac

Jared Roach roach at
Fri Sep 13 03:43:18 EST 1996

        As if we needed another one, right?

        However, I have found it useful, as have others in my
lab, so I felt it would only be fair to share it with everyone.

        So here's the help text from CrossMatcher, which should speak
for itself:

     This is a little Hypercard stack written to assist in 
comparing a set of DNA sequences with each other.  It is 
primarily designed to do cDNA comparisons, as there is an 
(arbitrary) limit of 1498 bp on sequence lengths (sequences 
can be longer but are ignored beyond 1498 bp).  No returns or 
spaces or other characters should be in the sequence files 
(or they will be treated as data).  Crossmatcher uses the 
dynamic clipping XFCN "DynaClip" which I wrote and is more 
fully described in my "DynaClip" stack.  
     Double-clicking on a highlighted selection in the results 
window brings up a dynamic alignment of each sequence along 
with the score of that alignment (which should be the same 
as the local alignment score - if not, you either need to 
increase the maximum alignment length or do a dot plot with 
some other program to unscramble multiple similarities)  The 
entry for maximum alignment cannot be set above 1999.  This 
is the maximum length that my XFCN DynaAlign can handle.  
However, this requires 8 Mb of RAM in addition to what HyperCard 
normally uses, so if you have HyperCard set to less RAM, you 
will want to cut back to around the default of 400, which 
requires less than 400 Kb of RAM in addition to the 1-2 Mb 
HyperCard needs.  The amount of RAM needed is proportional 
to the square of the sequence length.
      I strongly recommend using the default values for gap 
penalty, mismatch score, and match score.
     Adjusting the threshold will alter the number of matches 
returned.  Setting it to "1" will return all matches.

You can find CrossMatcher at:

Hopefully, someone will find it useful.

Jared C. Roach
Department of Molecular Biotechnology
Health Sciences Building, Room K354
University of Washington
Box 357730
Seattle, WA 98195
phone  (206) 616-4536
FAX    (206) 685-7301
roach at

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