Computational protocol: Genome-wide motif predictions of BCARR-box in the amino-acid repressed genes of Lactobacillus helveticus CM4

Similar protocols

Protocol publication

[…] A transcriptome analysis was performed using CM4 cells collected 0.5 h after the addition of casein hydrolysate and the cells were compared to those without the peptides in the fermented milk. Genes down-regulated by peptides over 30% compared to control cells cultured without peptides were selected for the analysis of the BCARR-box in the corresponding genes (Step 1). Then, to select specific genes that were repressed by the binding of a BCARR to the BCARR-box, a homolog of the predicted BCARR-box was searched by CLUSTALW and LALIGN analyses in the repressed genes (Step 2). Next, the BCARR-box found in the promoter region of the repressed genes was analyzed for the relationship between the location at the promoter region and the repressive effect (Step 3). Then, the palindromic structures of the predicted BCARR-boxes in highly and lowly repressed groups were compared (Step 4). […]

Pipeline specifications

Software tools Clustal W, LALIGN
Application Nucleotide sequence alignment
Chemicals Amino Acids