DNA motifs

     Selected Genome = Bacillus_subtilis_subsp_subtilis_str_168/ASM904v1_genomic     
Change active genome here


INTRODUCTION: A Transcription Factor Binding Site can be described in the form of a Position Frequency Table (PFM). In this section you can create your own PFM from an aligment; you can also search your genome using the PFM [PFM example]. The MOODS algorithm is used to screen for DNA motifs.
Paste your data in text box below:

Create PFM (Position Frequency Matrix) from alignment [alignment can be in fasta format or plain text]
Search PFM in intergenic regions only [using the PFM from text box above and the current active genome]
Search PFM in the whole genome [using the PFM from text box above and the current active genome]
Search Regular Expression in intergenic regions only [using the Regular Expression from text box above and the current active genome] ==> example
Search Regular Expression in the whole genome [using the Regular Expression from text box above and the current active genome] ==> example
BLAST DNA motif to whole genome (optimized short-blast) [ input is just a plain sequence. e.g. GATGATGATG ]
Add nearest downstream gene to motifs [first column should contain the start point of the motif]