【最新的131生物信息学web servers】v - PromH

PromH是Softberry 的系列软件之一，该组织就启动子预测就有几个软件了， 如TSSW，TSSG等。PromH是在TSSW的基础上改进的新的启动子预测软件。对启动子预测不仅考虑了几个保守的启动子元件，如TATA盒，同时也把转录因子结合位点作为一个因素。PromH还把不同物种的同源家族考虑在其中。这个是它的最大优点。
递交两条FASTA格式的不同种系的某基因上游的同源DNA序列，回来的结果直接显示在网页上。

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
...........

网址： http://www.softberry.com/berry.phtml?topic=promh
文献： http://nar.oupjournals.org/cgi/content/full/31/13/3540