>------------------------------ GENE-ID OUTPUT -------------------------------<
UPDATES:
1. New user-friendly interfaces available for Macintosh and Unix.
See help file for more info: send email 'help'
2. Help! We are trying to obtain funding for continued maintenance
and improvement of the GeneID server. If you think this server
deserves to be continued, please say so in an email to:
steen@bir.cedb.uwf.edu
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GENEID ONLINE SYSTEM FOR PREDICTION OF GENE STRUCTURE
version 1.1 3/1/1993
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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.
6. Estimated confidence of predicted exons is given.
Some of these enhancements are further described below.
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.
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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.
REGISTRATION:
No registration or user ID is required. Your return-path will be kept
on file for determining the number and geographical distribution of users.
SUBMITTING SEQUENCES:
Your sequences must be submitted in the following format (approximately same
format as used for fasta, BLAST and GRAIL):
You can submit only one sequence per mail. Put the sequence after the
keyword "Genomic Sequence" as shown below:
Genomic Sequence
>seqname
TTGGCCACTCCCTCTCTGCGCGCTCGCTCGCTCACTGAGGCCGGGCGACCAAAGGTCGCC
CGACGCCCGGGCTTTGCCCGGGCGGCCTCAGTGAGCGAGCGAGCGCGCAGAGAGGGAGTG
GCCAACTCCATCACTA...................
(Restrict the line length to 80 characters. The seqname is limited to 20
characters).
NOTE>> IF YOUR MAIL DOES NOT CONTAIN THE KEYWORD "GENOMIC SEQUENCE", OR
ANY OTHER KEYWORDS LISTED IN THIS FILE, NO MAIL WILL BE RETURNED TO YOU.
On a UNIX system you could send the File containing the sequence as
follows: mail -v geneid@bir.cedb.uwf.edu
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