Announcing GeneID 2.0: cDNA analysis, Blast analysis, etc....

Steen Knudsen steen at bir.cedb.uwf.edu
Fri Nov 19 17:28:11 EST 1993


             GENEID ONLINE SYSTEM FOR PREDICTION OF GENE STRUCTURE
                           version 2.0 11/14/1993
__________________________________________________________________________

The GeneID server, which analyzes vertebrate genomic DNA for exons and
genes,is now significantly improved:

1. GeneID now uses additional information in building gene models: the
   results of a protein database search (blastx). This has improved the
   accuracy significantly. This feature can be switched off with the
   option -noexonblast
2. The user can now specify information about known coding regions,
   first exons, or last exons, say from a partial cDNA. Examples:
   Genomic Sequence -known_coding 100 150
   Genomic Sequence -first_exon 33 67
   Genomic Sequence -last_exon 1007 1500
   GeneID will attempt to use that information in building and
   evaluating gene models.
3. The user can now experiment with alternative splicing by specifying
   regions where splicing is masked or blocked:
   Genomic Sequence -alt_splicing 120 170
   GeneID will then look for alternative splice sites outside that region.
4. Full list of available options:
   -small_output: Output only exons and gene models.
   -noexonblast : Switch off exon blast, and build gene models without
   -geneblast   : Compare top gene model to protein databases
   -known_coding: Specify region of known coding
   -first_exon  : Specify coordinates of known first exon
   -last_exon   : Specify coordinates of known last exon
   -alt_splicing: Specify region where splicing is blocked
   -NetGene     : Perform NetGene splice site analysis
5. A new, user friendly interface to GeneID is now available through
   Gopher. Point your Gopher to:
   name=Bioinformatics Resource Gopher
   host=dna.cedb.uwf.edu
   type=+
   For interactive DNA sequence analysis the TurboGopher 1.0.7 client for
   Macintosh is required (it is the only client we know of with all
   necessary "+" attributes. It is available from boombox.micro.umn.edu).
   Although this interface is still experimental, it makes it much easier
   to enter the correct format and select options.
6. GeneID now offers a separate analysis of cDNA sequences. Coding regions
   are predicted.

All these improvements are backwards compatible. Sequences submitted in
the old format will be procesed as usual (although with improved
accuracy).

For more information, send the email 'help' to geneid at bir.cedb.uwf.edu,
or retrieve the "GeneID Manual" from the Gopher Server.
__________________________________________________________________________

Steen Knudsen
Bioinformatics Resource
steen at bir.cedb.uwf.edu



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