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.
•
written
by
charlesgwellem •
1 answer
You could run FIMO on your entire genome for TFs (transcription factors; DNA-binding proteins) of interest, which gives you binding sites: genomic intervals where those TFs bind.
https://bioinformatics.stackexchange.com/a/2491/776
You can then map or intersect promoter regions with those TF binding sites with BEDOPS bedmap or bedops, respectively:
https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html
https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html
The use of bedmap is recommended to assign TFs to a promoter of interest. This tool will return both the promoter region and any TFs that overlap it by the specified overlap criteria.
Log in to answer this question.
-
Saccharomyces cerevisiae TFs
written by Deepblue •
-
Transcription factor binding site prediction
written by shwetamgr1 •
-
protein binding sites
written by yueli7
-
Accessing ENCODE data through R
written by salvatore.raieli2
-
Given a list of cell surface genes, is there a computational possibility to predict their interacti…
written by charlesgwellem •
-
Annotating non-coding DNA (CRM): TF binding site analysis
written by Sarthok •
-
Transcription factor binding site in Annovar
written by mangfu100
-
Best tool for finding transcription factor binding sites in a given genomic sequence
written by nash.claire
-
Advantages of Biobase's TRANSFAC over and above what is freely available?
written by fadsfadfdsafdasfdsa
-
How Do I Apply Tfbs Dna Motifs To A Genome?
written by Sam •
Cross-posted at SE: https://bioinformatics.stackexchange.com/questions/8691/how-do-i-computationally-predict-the-binding-position-of-a-dna-binding-protein-o/
You already received answers there, what about them?
Ok thanks saw it. I wish to find out about the existence of a simple user-friendly online tool, or an R package rather than methods that are more computationally intensive.
The suggested
fimoapproach is a bash one-liner on the command line. You won't find anything simpler :)Cross-posting the same question is generally discouraged. You could easily edit your Bioinformatics SE question to include these new parameters.