Hi RG members,
I am looking for a way to search a genome for a transcription factor (TF) binding site. Multiple studies have found that the TF binds to the consensus sequence DACCGGAAGTR so I would like to identify genes that have this sequence within 1000bp of their transcription state sites. I have found this site (http://motifmap.ics.uci.edu/) which does exactly what I want however, it does not have an option to find sites in a custom genome. I realise there are python programs available but I do not have any experience with this, I have some limited experience in R. Any suggestions of tools that I could use would be most appreciated. Thank you.
Dear Luke Simpson
These articles might be helpful, have a look:
1. Article Identification of the Binding Sites of Regulatory Proteins i...
2. Article Identifying transcriptional targets
3. https://www.yourgenome.org/facts/how-do-you-identify-the-genes-in-a-genome
4. https://www.nature.com/articles/ng1189
5. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0250592
Kind Regards
Qamar Ul Islam
After knowing the genes with any gene prediction method which would be good for the genome you are considering, Simply blast with a strict cutoff parameter such as e-value can help you.
Try looking at the history of transcription. Start with Jon Beckwith and the history of the lac operon
See the attached screenshot for a place to start. D. Booth
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