Similar softwares
Phylogenetic footprinting data
- Procedure:
We have also tested the performance of BOBRO against the other five programs on a set of orthologous promoters in E. coli K12 and a set of related genomes. For this test, we collected all promoter sequences from E. coli K12, containing 2,026 known cis motifs in RegulonDB. For each E. coli K12 promoter, we selected 12 orthologous promoter sequences from 675 complete bacterial genomes. Considering that each operon may be regulated by multiple transcription factors, we generated up to 10 motif candidates by each of the six programs for each data set. The prediction results (PC) by the seven normal programs are summarized in Figure 2.We further compared BOBRO with MicroFootprinter, which was specifically designed for motif finding on phylogenetic footprinting data, and specifically designed for prokaryotic genomes. we used a small set for comparison, which contains 10 transcription factors that regulate the most number of operons of E. coli K12, namely, CRP, Fur, FNR, IHF, Fis, Lrp, CpxR, ArcA, NarL and H-NS. Together they have 64 documented binding motifs according to RegulonDB. For these 10 datasets, we collected the prediction results of MicroFootprinter on its server and compared with those obtained by BOBRO (Figure 2).
- Results: (Figure 2)
Figure 2: Comparison between BOBRO and other programs on orthologous promoters across multiple genomes. The top panel shows the PCs of prediction results by the seven programs on 2,390 E. coli promoters. The lower panels are PC, SN and SP of prediction results by BOBRO and MicroFootprinter on promoters of 10 E. coli TFs
Page last updated: Apr. 29, 2010