Hi, Greetings! I have a list of K-mers (Human) like below
AAGTGCG
GGCGGCT
ACGTGGCA
TGCGTGGG
TGGCGTGA
Some of these K-mers may be serving as binding sites for TFs and some may be just the repeats. I want to annotate these K-mers with TFs. Wondering if there is a tool already which helps me get the outcome (without me converting it to fasta format and trying with PWMs) but would provide the Name of the TF, Accuracy of the site, The Actual Binding site Ideally like below
My Input Name of TF Accuaracy Actual Binding
GGCGGGAA E2F3 9.3/10 GGCGGGA
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ancient_learner
1 answer
There was a paper, published loooong back, that describes conversion of PWM to k-mers and assigns a score. A Novel Alignment-Free Method for Comparing Transcription Factor Binding Site Motifs
From the paper:
Here we describe a novel alignment-free method for quantifying the similarity of motifs using their PFMs by converting PFMs into k-mer vectors
So basically if you follow their methods, you can convert all your TFs PWM to k-mers with a score. Then you can do a direct overlap with your k-mers vs TFs derived k-mers. There are some tools implemented around this concept, you can search for them.
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