New TSSP program for Recognition of human Pol II promoter region
and start of transcription
Method description:
Algorithm predicts potential transcription start positions by linear
discriminant
function combining characteristics describing functional motifs and
oligonucleotide
composition of these sites. TSSP uses file with selected factor binding sites
from RegSite DB (Plants) developed by Softberry Inc. using literature data.
You can try TSSP at:
http://www.softberry.com/berry.phtml?topic=promoter
TSSP output:
First line - name of your sequence;
Second and Third lines - LDF threshold and the length of presented sequence
4th line - The number of predicted promoter regions
Next lines - positions of predicted sites, their 'weights' and TATA box
position
(if found)
Position shows the first nucleotide of the transcript (TSS position)
After that functional motifs are given for each predicted region; (+) or (-)
reflects the direct or complementary chain; S... means a particular motif
identificator from the Wingender data base.
For example:
tssp Wed Jul 10 02:52:32 EDT 2002
>gi|1902902|dbj|AB001920.1| Oryza sativa (japonica cultivar-group) gene for phos
Length of sequence- 5871
Thresholds for TATA+ promoters - 0.02, for TATA-/enhancers - 0.04
2 promoter/enhancer(s) are predicted
Promoter Pos: 1522 LDF- 0.13 TATA box at 1488 18.93
Enhancer Pos: 1597 LDF- 0.12
Transcription factor binding sites/RegSite DB:
for promoter at position - 1522
1468 (-) RSP00004 tagaCACGTaga
1459 (+) RSP00010 cACGTG
1456 (+) RSP00011 ctccACGTGgt
1461 (+) RSP00016 caTGCAC
1468 (-) RSP00016 caTGCAC
1256 (-) RSP00026 gcttttgaTGACtTcaaacac
1460 (+) RSP00065 ACGTGgcgc
1460 (+) RSP00066 ACGTGccgc
1459 (+) RSP00069 tACGTG
1341 (+) RSP00071 GACGTC
1346 (-) RSP00071 GACGTC
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