TSSP - Plant Promoter Identification program/ RegSite DB

softberry at softberry.com softberry at softberry.com
Wed Jul 10 13:54:00 EST 2002


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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