GeneID Online Server for Prediction of Gene Structure

Steen Knudsen steen at bir.cedb.uwf.edu
Thu Apr 29 08:44:57 EST 1993




          GENEID ONLINE SYSTEM FOR PREDICTION OF GENE STRUCTURE
                          version 1.1 3/1/1993

______________________________________________________________________

The GeneID server, which was first brought online at 
geneid at darwin.bu.edu in December 1991, has now had a few enhancements 
added:

1. It is now available at geneid at bir.cedb.uwf.edu as well.
2. Predicted gene models are automatically compared to protein 
   databases.
3. Several options can be supplied on the "command line" 
   (Genomic Sequence):
   -small_output : Mails only exons and gene models back to user.
   -all_exons    : Allows scanning for exons in small gene fragments.
   -noblast      : Turns off protein database search
   -netgene      : Send the file to netgene as well.
   Example:
     Genomic Sequence -noblast -small_output
4. Error handling has been improved to supply a more meaningful 
   feedback to the user, and be a little less unforgiving of user 
   error.  
5. The upper limit in sequence size has been increased from 20,000 bp 
   to 200,000 bp


NOTE that all these enhancements are backwards compatible. Requests 
submitted in the old format to geneid at darwin.bu.edu, will be processed 
along with requests containing new options.
______________________________________________________________________

GeneID is an Artificial Intelligence system for analyzing vertebrate 
genomic DNA and prediction of exons and gene structure (1). A 
prototype is implemented as a fast, automatic email-response system. 
Users have the option of having their DNA sequence analyzed by NetGene 
(2) simultaneously.

For more information, send the email 'help' to geneid at bir.cedb.uwf.edu


(1) Guigo, R., Knudsen, S., Drake, N., and Smith, T. (1992) Prediction
of Gene Structure. Journal of Molecular Biology. 226:141-157.
(2) Brunak, S., Engelbrecht, J., and Knudsen, S. (1991) Prediction of
Human mRNA Donor and Acceptor Sites from the DNA Sequence. Journal of 
Molecular Biology 220:49-65.


Steen Knudsen
Bioinformatics Resource
The University of West Florida
steen at bir.cedb.uwf.edu



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