How to use EPD33.seq database with the Wisconsin package?

Dan Jacobson danj at welchgate.welch.jhu.edu
Sat Feb 13 22:10:00 EST 1993


In article <1993Feb13.185547.27607 at gserv1.dl.ac.uk> ES at JII.AFRC.AC.UK writes:
>Dear helpers,
>I have got via FTP the file epd33.seq containing the Euk. Prom. database
>from the ncbi repository FTP archive, as suggested by Dan Jacobson recently
>on the net. I would like to perform a comparison of my favorite promoter
>sequence to this database. I have access here to the Wisconsin GCG
>package on a Vax. However if I use the Fasta implementation of GCG, it 
>does not recognize the format of the EPD33.seq database, and find
>no sequence to compare my sequence to. Knowing that I am a computer 
>hemi-imbecilus, can the net provide me with a simple and easy way to solve
>my problem. I would be forever gratefull.
>
>Jo the biologist 
>
>alias Eric Schoonejans (ES @ JII.AFRC.AC.UK)
> 

The database needs to be reformatted into GCG format before you can
use it with the GCG.  The solution is to get Don Gilbert's Readseq
which converts among many of the various sequence formats.  This is
not an uncommon question so I have gone ahead and done the conversion
to GCG format and placed it on my Gopher server.  If you would like
to retrieve the GCG formatted EPD - point your gopher client at
merlot.welch.jhu.edu and go to the

Selected Other Gophers and Information Servers/

directory and select the file -

EPD33.GCG


If you would like to get Readseq you can obtain it by gopher or
anonymous ftp from ftp.bio.indiana.edu.


Best of luck,

Dan Jacobson

danj at welchgate.welch.jhu.edu




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