Genefinder for the Masses -- Possibility or Hopeless Dream?

[Erich Schwarz]

    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.

    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.

    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