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.
