New Gene-Finder Plant gene prediction programs

Victor V. Solovyev solovyev at cmb.bcm.tmc.edu
Wed Oct 11 20:36:06 EST 1995


New BCM Gene-Finder service: 
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FGENEA, FEXA  and ASPL  Recognition of Plant gene structure 
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The parameters of prediction program were computed mostly by analysis of
                           Arabidopsis gene sequences
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	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

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The other services are 
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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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