Hi,
I am not very good at computational biology. I am working on a transcriptional repressor protein which is believed to be associated with virulence. I did DNAse 1 footprinting to determine the sequences it binds to a promoter and used the sequence to align promoter sequences from orthologous genes. I then used DMINDA to identify motifs. I want to scan the whole genome for predicting genes that are regulated by this particular transcription factor. Has anyone used DMINDA for whole genome scanning of a motif? I am not sure if I am doing it right, I uploaded the whole genome sequence in FASTA format, but it shows no hits. I also used DOOR to insert all promoter sequences of the organism and it doesn't work either :( Any suggestions please?
How did you specify the motif?
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DMINDA Motif Scan:
http://csbl.bmb.uga.edu/DMINDA/annotate.php#tabs-2
Motif format:
http://csbl.bmb.uga.edu/DMINDA/documentation.php?f=docs/user/faq.txt#f5
Hi Martin,
First, I used Motif finding to identify all the motifs. From the list of identified motifs, I selected (checked) one of them and proceeded to motif scan. The aligned sequences of the motif from orthologous genes were automatically transferred to the input query motifs box. I used both Matrix and Sequence alignment to scan for motifs. I then uploaded the whole genome sequence (NCBI) in FASTA format.
I determined the binding region using DNase 1 footprinting and used the sequence plus 15 bp flanking region from both 5' and 3' end to BLAST promoter sequences from other species. I can see about 14-16 bp are highly conserved from multiple sequence alignment. I then uploaded those sequences onto DMINDA for Motif finding, from the list of identified motifs I picked one, which was an inverted repeat.
Do you want the sequences?
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