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Alternatives To The Transfac Match Tool

Hi everybody,

has anyone ever work with the transfac command line tools?

I'm using the match tool for a search of binding sites for transcription factors with the goal of an enrichment analysis for the different motifs.

I would like to know if there are better tools to do the same analysis or maybe a tool to work with the output from the match tool

Thanks in advance

Assa

PS I am looking for tools for C. elegans

enrichment
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updated by Sean Davis Sean Davis • written by Assa Yeroslaviz Assa Yeroslaviz

1 answer

You might take a look at the Biostrings Bioconductor package. In particular, see if the matchPWM and countPWM do what you need.

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written by Sean Davis Sean Davis

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