New Yeast and Updated Gene_Finder Programs

Victor V. Solovyev solovyev at cmb.bcm.tmc.edu
Thu Dec 7 13:44:21 EST 1995


New and updated programs in BCM Gene-Finder service: 
==========================================================================
NEW: FEXY  and YSPL  Recognition of Yeast coding regions    
==========================================================================
	These 2 new programs were developed for analysis of Yeast sequences:
the programs are similar with Gene-finder programs for analysis of Human or 
Mammalian, Drosophila, Plant and Nematode sequences.   You can receive instructions 
about sequence format from WWW page
=================================================================================
 The other Gene-Finder programs were updated to predict single exon genes as well as 
 						exon-intron structure of multiexon genes.
----------------------------------------------------------------------------------

FEXY    - prediction of yeast 5'-, internal and 3'- potential exons

YSPL   - prediction of splice sites in yeast sequences

	Analysis of uncharacterized  sequences and help files are available 
through WWW: http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html

and by EMAIL server of Weizmann Institute of Science

Examples: mail -s fexy services at bioinformatics.weizmann.ac.il < test.seq
					where test.seq a file with the sequence.


(Soon analysis will be available from University of Houston also: 
						mail -s fexy  service at bchs.uh.edu < test.seq).

 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

FEXA - search for Yeast 5'-, internal and 3'-exons
ASPL - search for Yeast 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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