I'm trying to use Fire-pro to find motifs in linear motifs taken from ELM database. However, using the software, the syntax comes as follows:
perl $FIREPRODIR/fire_aa_wrapper.pl --expfile=<inp> --exptype=<type> --species=<sp> --runname=<dir/prefix>
where inp indicates the input expression profile. Now for any given linear motif, say for instance we take the MOD_SUMO identifier and one can download all the instances of it from ELM. So then when you have a fasta file with all the sequences, each containing the motif, how would one go about running fire-pro against it? To be able to run firepro one first needs the input expression profile, where can I find it? Thanks!