NEW !!!!!!!!!!! high accuracy SS prediction for single sequences
SSPAL- Prediction of protein secondary sturcture by using local alignments
Accuracy:
Overall 3-states (a, b, c) prediction gives 71% correctly predicted residues on
126 and 471 non-homologous proteins using the jack-knife test procedure. THIS ACCURACY
IS REACHED WITHOUT USING MULTIPLE ALIGNMENT INPUT
Implemented on WWW: http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html
On DEC-alpha it takes a minit,but unfortunately on very loaded
Sun Baylor computer you have to wait longer
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================== The other services are ===============================================================
FGEBEHB - search for Mammalian gene structure with exons assembling by dynamic programming and
using similarity information with known proteins by data base scaning with fasta
FEXHB - search for Mammalian coding exons using exon recognition functions and similarity information
with known proteins by data base scaning with fasta
(the above 2 programs available only by ftp loading to your local computer!!!)
You can ftp from gc.bcm.tmc.edu 3 programs for Human and Bacterial
gene prediction. The programs better run on DEC_alpha and available from dec_...
directories. Variants for Sun OS 5 and OS 4 will be in sun5_.. and sun4_ dirs.
Make: ftp gc.bcm.tmc.edu
cd pub/solovyev
and then cd dec_fgenehb or dec_fexhb or dec_cdsb
copy the stuff from these directories to your separate directories.
Some additional information about Gene-Finder programs you can get from:
WWW: http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html
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
WWW address: http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html
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.
SSPAL - Prediction of secondary structure by nearest-neighbor method using local alignments
PSITE - search for PROSITE patterns with statistics
