PromH(G) Recognition of human and animal Pol II promoters

(Transcription Start Site and TATA-box)

Method description
To further improve promoter identification accuracy achieved by TSSG program, we developed a new program, promH(G), by extending the TSSG program feature set. PromH uses linear discriminant functions that take into account, in addition to features realized in TSSG, conservation features of major promoter functional components, such as transcription start points, TATA-boxes and regulatory motifs, in pairs of orthologous genes aligned by SCAN2 program.
PromH(G) output
OUTPUT file begins with description of the program allocation, used abbreviations and Search Parameters (Lines 1-10). Next two lines include name and length of the first query sequence and the number of predicted promoter regions. Then, positions of predicted sites, their "weights" and TATA-box position (for TATA promoters) are given. After that, functional motifs are given for every predicted region; (+) and (-) reflect direct or complementary chain; $... means a particular motif identificator from Transcription Factors Database, TFD (Ghosh, Nucleic Acids Res., 1993 , 21, 3117-3118). Then, the same information is given for second query sequence.

Example of output file

      Program  promHG  (Softberry Inc.)
      Search for TATA+/TATA- promoters in 2 aligned DNA sequences

  NOTE: PHa  - Homology Level of Aligned Sequences in LOCAL Search Area (-100,TSS+40)
        PHs  - Homology Level of Aligned Sequences around TSS
        PHss - Homology Level of Aligned Sequences to Right from TSS
        PHt  - Homology Level of TATA-boxes in Aligned Sequences
        PHr  - Mean Homology Level of Regulatory Elements in LOCAL Search Area

    Initial / Final Thresholds -   2.00 /  6.00
 ======================================================================
 >H-NPPA/AL021155/[33199:35843/
  Length of sequence-      2645
        1 promoter(s) have been predicted
  Promoter Pos:   2549 (Weight - 16.00)   TATA box at:   2517 (Weight -   218.33)
      PHa -  78%   PHs - 100%   PHss -  74%   PHt - 100%   PHr -  80%
  Transcription factor binding sites:
 for promoter at position -    2549
   2462 (+) S01152       AAGTGA
   2378 (+) S00922       AGAGG
   2525 (+) S00922       AGAGG
   2306 (-) S00922       AGAGG
   2499 (-) S00395       CACGCW
 ..............


 --------------------------------------------------
 >R-NPPA/J03267/[1638:3722]/-2000:+85/CDS: 3723, premRNA: 3638                   
 Length of sequence-      2087
        2 promoter(s) have been predicted
  Promoter Pos:   2000 (Weight - 15.59)   TATA box at:   1970 (Weight -   217.73)
      PHa -  78%   PHs - 100%   PHss -  77%   PHt - 100%   PHr -  89%
  Promoter Pos:   1662 (Weight:   6.37)
      PHa -  76%   PHs -  88%   PHss -  72%   PHr -  74%
  Transcription factor binding sites:
 for promoter at position -    2000
   1915 (+) S01152       AAGTGA
   1773 (-) S00922       AGAGG
   1716 (+) S00392       AGGAAG
   1999 (-) S02113       CCAGCTG
   1713 (+) S01003       CCCAG
 ...........
 for promoter at position -    1662
   1504 (+) S01090       AATGA
   1610 (+) S01013       ACAGCTG
   1484 (+) S00922       AGAGG
   1505 (+) S01444       ATGAATCAG
 ...........