Help with dna sequence files

Brian Fristensky frist at cc.umanitoba.ca
Thu Mar 12 10:59:54 EST 1998


Floyd Martin wrote:

> Hello there!
>         I am a graduate student at Ohio State University (Biophysics
> program).  I am interested in studying intron sequences of DNA.
> Unfortunately, I have little or no idea as to how to go about extracting
> said introns from files that Genbank, etc. have collected.  I have seen
> numerous articles that have done so but their practical description was
> less than detailed.
>         I guess what I'm getting at here (assuming I'm even adressing the
> right people) is there any software out there that can do it for me or
> perhaps put the data files into a more friendly format?  If this is a do it
> yourself enterprise, could someone give me a general idea of how to
> proceed?  I'm totally flummoxed here.  Any assistance would be greatly
> appreciated.
>
> floyd martin (martin.687 at osu.edu)

 The FEATURES program of the XYLEM package can do what you
want. FEATURES can extract sequences from GenBank entries
using any Feature Key (eg. intron, mRNA, CDS, rRNA, exon....).
Even features that are derived from many entries can be
correctly assembled in an automated fashion. Perhaps importantly,
FEATURES can work on large groups of GenBank entries at
a time. So if you have 200 GenBank entries and you want all the
introns or exons extracted, that can be done in one step.

For more information, see

http://home.cc.umanitoba.ca/~psgendb/XYLEM.html

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Brian Fristensky                |
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