Alternatives To The Transfac Match Tool

Question

[Assa Yeroslaviz]

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

Answer 1

[Sean Davis]

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