Program Promoter 2 makes a marginal prediction (score 0.613) of a promoter between 200 300 bp upstream.
Sessions are led by one of the participating managers or professionals, supported by a mentor from the program promoter agency (PHDM).
To verify if the latter peak is caused by the presence of a similar TATA motif we have classified the promoters into two groups: TATA containing (TATA+) and TATA-less (TATA-) group using program Promoter Classifier [ 39].
Found CpG islands that accumulate in three distinct zones of the analyzed 5' site of the SIP1 gene are represented in Figure 5. Analysis of the same region by a promoter prediction program, Promoter 2.0 [ 39], revealed three previously described promoter candidates [ 42, 43].
We then predicted the p53 binding sites on promoter region of Malat1 using "PROMO" program (Promoter 2.0 Prediction Server), two typical p53 binding domains have been predicated that the region of (−698 to−669 bp) named as p53-BS-1 locus, the region of (−656 to−625 bp) named as p53-BS-2 locus (Figs. 6a and 6b).
The programs PromoterInspector, McPromoter and NNPP predicted no promoters in the 2000 bp region upstream of the GenBank start point for the human GABAAπ subunit gene sequence.
In order to search for a putative promoter region, GenBank DNA sequence for the human β2 subunit gene was searched using the programs PromoterInspector, NNPP, Promoter 2 and McPromoter, within a region extending from 2000 bp upstream of the mRNA start point to approximately 500 bp downstream.
It also capitalizes on the experiential knowledge of the program's promoters.
For this, we used the BCRANK program with promoters of genes repressed by Mig1 and Mig2, ordered by redundancy.
We used Visual Basic to develop a software program for promoter analysis - called PromKappa (Promoter analysis by Kappa), and a software program for sorting promoter patterns - called PromNN (Promoter analysis by Neural Network).
