New Gene-Finder Plant gene prediction programs

Victor V. Solovyev solovyev at cmb.bcm.tmc.edu
Wed Oct 11 17:18:14 EST 1995

New BCM Gene-Finder service: 
FGENEA, FEXA  and ASPL  Recognition of Plant gene structure 
The parameters of prediction program were computed mostly by analysis of
                           Arabidopsis gene sequences
	These three new program developed for analysis of Plant sequences:
the programs are similar with Gene-finder programs that were developed earlier for
analysis of Human or Mammalian sequences.   You can receive instruction about sequence 
format from WWW page

FGENEA -prediction of gene structure with assembling of potential exons

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

ASPL   - 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

 and soon will be available by sending your file containing a sequence 
(the sequence format is described below) to Weizmann Institute of Science Email services:

 services at bioinformatics.weizmann.ac.il

and to University of Houston: service at bchs.uh.edu 

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

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

where test.seq a file with the sequence.

The same for FEXA and ASPL 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 Drosophila gene structure with exons assembling by dynamic programming
FEXD - search for Drosophila 5'-, internal and 3'-exons
DSPL - search for Drosophila splice sites

FGENEN - search for Nematode gene structure with exons assembling by dynamic programming
FEXN - search for Nematode 5'-, internal and 3'-exons
NSPL - search for Nematode splice sites

FGENEA - search for Plant gene structure with exons assembling by dynamic programming
FEXA - search for Plant 5'-, internal and 3'-exons
ASPL - search for Plant 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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