Need Base Count software for Mac

mathog at seqaxp.bio.caltech.edu mathog at seqaxp.bio.caltech.edu
Tue Sep 5 12:24:33 EST 1995


In article <v01530500ac722a2d443a@[140.254.12.85]>, rumpf.1 at osu.edu (Robert Rumpf) writes:
>We need a program that will tell us the GC content (in percent) of a
>sequence...I downloaded GATCcount from IUBIO but it won't run on our Macs
>(we're using system 7.5).  Any ideas?  TIA...
>

This is pretty crude, but if you only need to do this once and a while you
can carry out the calculation with just about any word processor. 

1.  Edit out all the comments and numbers on a COPY of the file.
2.  Make two copies from that: GC, AT
3.  On GC,
    global search and replace "A"->nothing
    global search and replace "T"->nothing
    use word count (it it can count characters in a document.)
    Word count only counts words and lines? -> replace G with G<return>
    replace C with C<return>.  Replace <return><return> with <return>,
    run word count
4.  AT, as for GC (you figure it out!)
5.  %GC = (100 * GC)/(GC + AT)  with a calculator or long hand division.

Regards,

David Mathog
mathog at seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 




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