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Integrated Genome Viewer "Motif Finder" like-tool for the command line?

I recently asked about help finding promoters in particular, and got a helpful pointer for that... however, it wasn't exactly what I wanted I found out.

I then found something much closer to what I wanted: the Integrated Genome Viewer has a "Motif Finder" tool, and you can even enter in ambiguous nucleotides to it. The only catch (for me at least) is... is there a command line tool like it? Do I have to interact with IGV through the GUI? It seems there is some command line support for IGV, but it seems like it is geared more for pre-processing. Sorry if I missed something though, would appreciate any pointers!

genome sequence
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updated by danvoronov • danvoronov • written by ccc • ccc

1 answer

If any useful, I wrote fastaRegexFinder for this.

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written by dariober dariober

This sounds exactly what I was looking for! Much appreciated :)

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written by ccc • ccc

Does it work with IUPAC codes, i.e. does it find sequences with a G or T if I input K into regex? For instance, my fasta would be ATGGTACAATTGC, would using -r KKTAC return a GGTAC from the sequence? It would be useful since most genomic sequences only use ATGC while most transcription factor motifs use IUPAC ambiguity codes.

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written by danvoronov • danvoronov

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