de novo Transcription Factor Discovery for a Single Gene

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2.9 years ago

Sai Prasada • 0

Hi! I am trying to perform de novo motif discovery of a single genes, but I am a little unsure of which algorithm to use. The most common one appears to be HOMER, but the instruction manual says that there needs to be multiple input sequences for it to work. I currently have only a FASTA file for my single gene. Any help on how to proceed forward would be much appreciated.

Analysis FASTA Motif Transcription Factor • 619 views

ADD COMMENT • link updated 2.9 years ago by Michael 55k • written 2.9 years ago by Sai Prasada • 0

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I am quite sure this doesn't work. You can either: find known motif in a single (or any) sequence OR discover new motif from multiple sequences. If you think about it, it's quite logical. A motif is a pattern that is common to a set of sequences, you cannot generalize based on a single observation.

ADD REPLY • link 2.9 years ago by Michael 55k

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