I am trying to find which genes share a specific motif that is used by a protein to modify transcription of a gene. What I want to find is all genes that have such a motif in their cis-regulatory sequence. What would be the best software to use for this?
To add, I work on Drosophila.
There are quite a few online tools for cis-element identification, mapping and analysis. Some well characterized species such as Drosophila and Humans have tools specific for that species (you'll have to look up your species)...but my favourite suite of tools is hosted at RSA-tools (http://rsat.ulb.ac.be/).
It does matter because motif identification software and databases are created based on specific organisms so plant regulatory motifs have completely different databases than other organisms like softberry, transfac, etc
I checked out the MEME software, and it cannot do what I need to do. It can find new motif's in a bunch of sequences, or I can find whether a motif has been found already, or I can match GO functions with a motif, but I do not see how I can get a list of genes.
The RSA tools are much more helpful, and can indeed do what I need to do. With great success, so that you for the help.
If you have ChIP data, MatrixREDUCE with give you DNA binding motifs with binding energies.
http://bussemaker.bio.columbia.edu/software/MatrixREDUCE/
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