I need a tool or a function I can use in my code (R, or Python) that I can cross reference a MOTIF against known MOTIFS, a function that will take as input a MOTIF (a probability weight matrix, PWM which is a 4 by m matrix for an m-length motif) and spit out the closest -n- known motif(s). Is there such a function/tool or something close to it? Thanks much.
A popular tool for doing this is tomtom, part of the meme package.
You can try it via interactive web form here.
Once installed locally it can be run via command line
Additionally, it is available in the Bioconductor package
memes as explained in Motif Comparison using TomTom
Answer from @m, converted from comment:
Hi @ZebraFish Motifs package Biopython