pombe genefinder parameters

Kay Hofmann khofmann at isrec-sun1.unil.ch
Wed Feb 14 16:01:03 EST 1996


Can anybody point me to a parameter set that is useful for the
genefinder program built into Pombase/AceDB ?
The default parameters either are not good or I make a stupid error:
No matter what I do, the genefinder always wants to make one gene
containing lots of introns of the whole DNA fragment, even of the
whole cosmids. If I restrict the range, the program always tries to
make one gene covering the total range. I would have thought that
the program is able to stop with a gene if the introns are getting
too long.
Another annoying thing: if there are long, uninterrupted ORFs which
I know to contain no introns, the genefinder program always forces
some mini-introns into the ORFs.
I tried to modify the parameters, but did not get any decent results.

Many thanks in advance,

Kay


-------------------------------------------------------------------
Dr. Kay Hofmann                              Tel. +41 (21) 692-5892
Bioinformatics Group                         FAX  +41 (21) 652-6933
ISREC
CH-1066 Epalinges s/Lausanne
Switzerland                     E-mail: khofmann at isrec-sun1.unil.ch



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