From usenet.ucs.indiana.edu!sol.ctr.columbia.edu!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!uunet!oracle!biosci!bir.cedb.uwf.edu Fri Apr 30 23:04:41 EST 1993 Article: 377 of bionet.announce Path: usenet.ucs.indiana.edu!sol.ctr.columbia.edu!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!uunet!oracle!biosci!bir.cedb.uwf.edu From: steen@bir.cedb.uwf.edu (Steen Knudsen) Newsgroups: bionet.announce Subject: GeneID Online Server for Prediction of Gene Structure Message-ID: Date: 29 Apr 93 13:44:57 GMT Sender: kristoff@net.bio.net Distribution: bionet Organization: Bioinformatics Resource, UWF Lines: 55 Approved: bionews-moderator@net.bio.net GENEID ONLINE SYSTEM FOR PREDICTION OF GENE STRUCTURE version 1.1 3/1/1993 ______________________________________________________________________ The GeneID server, which was first brought online at geneid@darwin.bu.edu in December 1991, has now had a few enhancements added: 1. It is now available at geneid@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@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@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@bir.cedb.uwf.edu