New Drosophila/Nematode Gene-Finder Programs

Victor V. Solovyev solovyev at cmb.bcm.tmc.edu
Thu Oct 5 16:32:42 EST 1995


New BCM Gene-Finder service: 
==========================================================================
FGENED, FEXD  and DSPL  Recognition of Ivertebrate (Drosophila/Nematode) gene structure 
==========================================================================
	These three new program developed for analysis of Invertebrate sequences:
the programs are similar with Gene-finder programs that were developed earlier for
analysis of Human or Mammalian sequences. They work for Drosophila as well as for 
Nematode sequences.  You can receive instruction about sequence format from WWW page

FGENED -prediction of gene structure with assembling of potential exons

FEXD    - prediction of 5'-, internal and 3'- potential exons

DSPL   - prediction of splice sites

	Analysis of uncharacterized  sequences and help files are available 
through WWW: http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html

 or by sending your file containing a sequence 
(the sequence format is described below)  Weizmann Institute of Science Email services:

 services at bioinformatics.weizmann.ac.il

(and soon will be available in University of Houston: service at bchs.uh.edu )

Examples: mail -s fgened services at bioinformatics.weizmann.ac.il < test.seq

or mail -s fgened  service at bchs.uh.edu < test.seq

where test.seq a file with the sequence.

The same for FEXD and DSPL programs.
 

Questions:solovyev at cmb.bcm.tmc.edu

===============================================================
The other services are 
===============================================================
FGENEH - search for Mammalian gene structure with exons assembling by dynamic programming 
FEXH   - search for 5'-, internal and 3'-exons
HEXON  - search for internal exons 
HSPL   - search for splice sites
RNASPL - prediction exon-exon junctions in cDNA sequences
CDSB   - prediction of Bacterial coding regions
HBR    - recognition of human and bacterial sequences to test a library 
         for E. coli contamination by sequencing example clones
TSSG   - recognition of human promoter regions (Ghosh/Prestridge motif data)
TSSW   - recognition of human promoter regions (Weingender motif data base) 
POLYAH - recognition of of 3'-end cleavage and polyadenilation region
         of human mRNA precursors

FGENED - search for Invertebrate gene structure with exons assembling by dynamic programming
FEXD - search for Invertebrate 5'-, internal and 3'-exons
DSPL - search for Invertebrate splice sites

SSP    - prediction of a-helix and b-strand in globular proteins
	 by segment-oriented approach.
NSSP   - prediction of a-helix and b-strand segments in globular proteins
         by nearest-neighbor algorithm.







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