GENEID - Online Prediction of Gene Structure

[Steen Knudsen]

In <1991Dec3.110139.131736 at rrz.uni-koeln.de> 
KHOFMANN at cipvax.biolan.Uni-Koeln.DE (Kay Hofmann) writes:

>Well, when i saw the two announcements (and before i started reading them
>thoroughly) i also had the impression that GRAIL and GENEID do the same 
thing.
>
>Both try to find exons in large stretches of DNA, but their approaches are
>completely different. 
>

>
>To compare both programs, it tried them with the only long and completely 
>sequenced gene from our lab. It is 18kb long and contains 7 exons. The 
first
>one is extremely short (4bp), the rest ranging between 80 and 200 bps. 
There is
>one large intron of appr. 12kb and some shorter ones.
>
> .....

I would like to thank Kay Hofmann for his independent comparison of GRAIL 
and GENEID, and for pointing out some unnecessary constraints on the 
sequence format for GENEID. We have now changed GENEID to accept the 
following characters in the sequence: 
[gacturymckswhbvdnxGACTURYMCKSWHBVDNX]
Other updates will be posted in the reply mail files from GENEID.

I would like to add to Kay Hofmanns description of GENEID, that it does 
in fact analyze some 30 parameters for each potential exon. These parameters
are compared to known exons from 169 vertebrate genes from GenBank, and
used to decide whether it is an exon or not, and for ranking the exons.

GENEID is an ongoing development, so I would appreciate further feedback 
from the users (47 registered users 3 days after the original posting).


Steen Knudsen (on behalf of the GENEID Gang)
Biomolecular Engineering Research Center
Boston University.