Hi all,
Has anyone here used FirePro motif finder? If so, can anyone show me an example of where one can take a sequence of multiple instances of one motif from ELM database and convert it to the data that FirePro needs?
Firepro requires data so that:
The data input to FIRE-pro is a "protein profile" (i.e. a two-column file with the name of the protein and a number) and the program needs to have a pre-loaded fasta file with sequences corresponding to the protein-names. It's a slightly different set-up than most protein motif finders, which just have a fasta file as input. From what organism is the data you are analyzing? Presumably, you'll want to create a profile in which all the proteins from your fasta file are labeled as "1", and all other proteins are labeled as "0".
I would be very grateful if someone can show me how to use that one software which I really need for some work.
FIRE-pro looks very interesting. I note that in the FIRE-pro paper they compare the results of a FIRE-pro analysis to the patterns in ELM (http://elm.eu.org/). So it is probably worth asking the FIRE-pro folks, and possibly the ELM folks too, for advise on how to do this (give them a pointer to this question so they can provide feedback too).