TSSP - Plant Promoter Identification program/ RegSite DB

softberry at softberry.com softberry at softberry.com
Thu Jul 11 05:27:27 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 
function combining characteristics describing functional motifs and 
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:

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 
 (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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