I wish to find out if HOMER tool can be used to predict the binding site of a transcription factor on a list of DNA sequences.
Thank you in advance for your kind and helpful responses.
Dear Anchang Charles Gwellem
I hope this note finds you well.
First, please check PDNAsite server (https://www.nature.com/articles/srep27653). It can support you to know which parts of a protein strongly have a tendency to interact with the target DNA molecules. Similarly, another option for you is StackDPPred server (https://bmll.cs.uno.edu/add) that freely available for academic users.
Next, DNAbinder (http://crdd.osdd.net/raghava/dnabinder/), DP-bind (http://lcg.rit.albany.edu/dp-bind/) and some other servers or offline tools can also provide a user-friendly platform to handle your project. More importantly, there are some python scripts in the literature for prediction the position of DNA-binding proteins.
If I was true, I think Rostlab in Munich recently developed a python script for prediction of DNA-binding proteins. You can check their homepage or their page in GitHub for finding that script I discussed. Their script can predict the position of DNA-binding proteins through amino acid sequence.
Before choosing software in this field, you should be assuring about the sensitivity of target tools for prediction of DNA-binding residues. All in all, the sensitivity of applied algorithm in such servers or tools must be over %60, respectively. By and large, I think you should try to delve the literature to find other suitable tools for your purpose.
Regards,
HR
Yes you can use Homer or the MEME suite, or some other tools that might be available.
Dear Anchang Charles Gwellem,
Yes, HOMER is an excellent tools for such tasks. Here you can find a nice tutorial:
http://homer.ucsd.edu/homer/ngs/peakMotifs.html
This will show you how to carry out a so-called de novo motif analysis and find the most frequent motifs under your sequences of interest in an unbiased manner (no database used prior to searching - only at the end for comparison).
Best luck with it!
Best regards,
Attila
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