Method description
To improve promoter identification accuracy achieved by TSSW
program, we developed a new program, promH(W), by extending the TSSW program
feature set. PromH uses linear discriminant functions that take into account,
in addition to features realized in TSSW, conserved 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.
The program was tested on two sets of pairs of orthologous, mostly human and
rodent, sequences with known transcription start sites (TSS), annotated to have
TATA (21 genes) or TATA-less promoters (38 genes). For the first set, promH(W)
correctly predicted TSS for all 21 genes with a median deviation of 2 bp from
annotated site location. Only for two genes, there was significant (46 and 105
bp) discrepancy between predicted and annotated TSS positions. For the second
set of TATA-less promoters, TSS was predicted for 27 genes, in 14 cases within
10 bp distance from annotated TSS, and in 21 cases - within 100 bp distance.
Despite more discrepancies between predicted and annotated TSS for genes from
the second set, these results are consistent with observations of much higher
occurrence of multiple TSS in TATA-less promoters.
Due to TRANSFAC license limitations, only academic users are allowed to access PromH(W) at our site.
PromH(W) output
An output file begins with description of the Program's allocation, used abbreviations
and search parameters (Lines 1-11). Next two lines includes 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; $... means a particular
motif identificator from TRANSFAC database (Wingender et al., Nucleic Acids
Res., 2001, 28, 316-319). Then, the same information is given for second query
sequence.
Example of output file
Program promHW (Softberry Inc.)
Search for TATA+/TATA- promoters in 2 aligned DNA sequences
NOTE: PHa - Homology Level of Aligned Sequences in LOCAL Search Area (-100,TSS+40)
PHs - Homology Level of Aligned Sequences around TSS
PHss - Homology Level of Aligned Sequences to Right from TSS
PHt - Homology Level of TATA-boxes in Aligned Sequences
PHr - Mean Homology Level of Regulatory Elements in LOCAL Search Area
Initial / Final Thresholds for TATA+ promoters - 0.10 / 2.50
Initial / Final Thresholds for TATA-/enhancers - 0.70 / 3.70
===========================================================================
>h-PGAM2 [1:962]/-920:61/ AC J05073
Length of sequence- 981
2 promoter/enhancer(s) have been predicted
Enhancer Pos: 899 (Weight: 5.79)
PHa - 68% PHs - 100% PHss - 22% PHr - 76%
Promoter Pos: 921 (Weight - 3.61) TATA box at: 895 (Weight - 18.51)
PHa - 66% PHs - 77% PHss - 23% PHt - 70% PHr - 71%
Transcription factor binding sites:
for promoter at position - 921
752 (+) MAIZE$ADH1 CGTGG
631 (+) Y$ADH2_01 TCTCC
854 (+) HS$ALBU_02 TTGGCA
853 (+) MOUSE$A21C ATTGG
824 (+) MOUSE$MCK_ cccaaCACCTGCtgcctgagcc
...................
--------------------------------------------------
>r-PGAM2 [-1181..+800: 1:2160] AC Z17319/
Length of sequence- 1300
2 promoter/enhancer(s) have been predicted
Enhancer Pos: 1123 (Weight: 3.97)
PHa - 68% PHs - 100% PHss - 22% PHr - 80%
Promoter Pos: 1148 (Weight - 2.83) TATA box at: 1119 (Weight - 17.83)
PHa - 65% PHs - 88% PHss - 23% PHt - 70% PHr - 82%
Transcription factor binding sites:
for promoter at position - 1148
902 (+) Y$ADH2_01 TCTCC
935 (+) HS$ALBU_02 TTGGCA
1081 (+) MOUSE$A21C ATTGG
942 (+) RAT$EAI_08 ccctgccCAGCTGgc
........................................