New high accuracy Protein SS prediction for single sequence

Victor V. Solovyev solovyev at cmb.bcm.tmc.edu
Wed Sep 11 20:14:28 EST 1996


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
=================================================================================

================== 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







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