New WWW,Email service:POLYAH - Recognition of 3'-end cleavage and polyadenilation region
Victor V. Solovyev
solovyev at cmb.bcm.tmc.edu
Thu Aug 31 14:10:01 EST 1995
New BCM Gene-Finder service:
POLYAH - Recognition of 3'-end cleavage and polyadenilation region
of human mRNA precursors
Department of Cell Biology, Baylor College of Medicine
Analysis of uncharacterized human sequences is available
through WWW: http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html
or by sending your file containing a sequence
(the sequence format is described below) to University of Houston
and soon to Weizmann Institute of Science Email services:
service at bchs.uh.edu or services at bioinformatics.weizmann.ac.il
with the subject line "polyah".
Examples: mail -s polyah service at bchs.uh.edu < test.seq
mail -s polyah services at bioinformatics.weizmann.ac.il < test.seq
where test.seq a file with the sequence.
Algorithm predicts potential position poly-A region by linear discriminant
functions combining characteristics describing various contextual
features of these sites. The default LDF threshold in the server is equal 0.
The accuracy has been estimated for the set of 131 poly-A reegions
and 1466 non-poly-A regions of human genes, having AATAAA
For 86% accuracy poly-A region prediction the algorithm has 8% false
predictions (Sp=50%; C=0.62). For example, with threshold 0.7 it
predicts 8 of 9 poly-A sites of AD2 genome (35937 bp.) and overpredict
4 false (Compare with method of poly-A site prediction
(CABIOS 1994,10,597-603), which for
8 true predicted sites gives 968 false positive sites).
SUBMITTING SEQUENCES VIA EMAIL:
For email submission the sequences must have the following format:
Name of your sequence
(The line length must be less than 80 letters).
You have to send the file containing the sequence to:
service at theory.bchs.uh.edu
Subject line must be:polyah
Example: mail -s polyah service at bchs.uh.edu < test.seq
1st line - name of your sequence; 2nd line - Length of your sequence
Next lines - positions of predicted sites and their 'weights',
Position shows the first nucleotide of the AATAAA consensus in the
HSG11C4A 1741 bp DNA PRI 21-FEB
Length of sequence- 1741
1 potential polyA site was predicted
Pos.: 988 LDF- 4.06
Salamov A.A., Lawrence C.B., Solovyev V.V. Recognition of
3'-end cleavage and polyadenilation region of human mRNA precursors.
(1995) (in preparation).
Questions:solovyev at cmb.bcm.tmc.edu
The other services are
FGENEH - search for 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
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.
More information about the Bionews