Genefinder for the Masses -- Possibility or Hopeless Dream?

burglin at ubaclu.unibas.ch burglin at ubaclu.unibas.ch
Mon Aug 12 12:47:09 EST 1996


>     I've been trying to get BLAST data from a partially sequenced
> cosmid that's of interest to our lab, and I've been forced to the
> following realization:
> 
>     The public BLAST servers *really* don't like you if you try
> to search reasonably sized chunks of DNA.  I got NCBI to search
> 9 kb exactly once, but it took God's own time, and the output
> got yanked away between when I saw it came up and when I would
> have been able to download it.  Fooey on that.

Well, 9kb is pretty big,if NCBI doesn't handle it, hardly anybody
else will...
Anyway, if you trimmed down an interesting region to
a few cosmids, you probably would want to trim the rescue
down to 20 kb or so... , there is no point in hunting
down interesting open reading frames if they are not your
gene anaway...


>     So.  Does anybody out there know if there's either a publicly
> available server or a transferrable version of _C. elegans_
> Genefinder that we could use here at Columbia on cosmid sequences?
> If there was just a way to distill 40 kb of DNA to a few
> possible proteins, BLAST searching the residue would be a joy.
> 
How about being more explicit, this information is no help at all.
Just get acedb, and you have genefinder in there to
do all the open reading frame analysis you need.
and as you say, with the ORFs it's easy to do a blast.


>     Thank you for any advice.  I'm sure there's an obvious
> answer, but this seems to be my day to be computer illiterate.
> 
> 
> --Erich Schwarz
>   schwarz at cubsps.bio.columbia.edu

Thomas Burglin





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