pombe genefinder parameters

Yeasties PomBase Database pombase
Thu Feb 15 06:47:54 EST 1996

Genefinder was added to ACEDB specifically for the C. elegans genome
sequencing project. GeneFinder is tuned for different organisms by
changing Feature and AutoFind parameters. This will work to some
extent for S. pombe but there are some crucial problems.

1. The Autofind Parameter "Intron rate per log bp" is hard coded for
C. elegans. 

GeneFinder imposes a penalty, the "intron cost", for introns within
the range 30-55 bp and adds an additional penalty according to the
parameter "intron rate per log bp" for introns >55 bp. The 55 bp limit
is too short for S. pombe genefinding in our experience. This "zone
for short introns" will change to an AutoFind Parameter in future
versions of ACEDB and will make GeneFinder more applicable to other
organisms. We expect to have this feature in the next release of
PomBase (4-2).

2. GeneFinder does not know about splice branch sites

S. pombe has well conserved splice branch sites, unlike C. elegans. It
is possible to trick GeneFinder into using a combination of splice
branch/acceptor by reading these onto the Fmap as SPLICE_3 user
segments (usegs). We intend to make available a program to calculate
these branch/acceptor motifs with the next realease of PomBase (4-2).

In the meantime, try increasing the AutoFind parameter intron cost but
don't expect miracles.

Note. PomBase version 4-1 was released on 13th Feb and is avialable
from ftp.sanger.ac.uk in directory pub/PomBase

Sean Walsh

                             | Sean Walsh    
   email: svw at sanger.ac.uk   | The Sanger Centre
   tel: 01223 494955         | Hinxton Hall     
   fax: 01223 494919         | Hinxton	         
                             | Cambridge CB10 1RQ         

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