I would like to search an unannotated genome for all amino acid transporters (pfam:PF01490). Whats the most effective way of doing this, blast sounds easy but the proteins are multi exon, I was thinking using hmm's but not sure how and if best option given searching genome. Can anyone recommend and maybe example linux commands etc.
You can use tblastn and search the proteins in your database against the genome. If you want to scan peptides using HMM you can use interproscan.sh from http://www.ebi.ac.uk/interpro/download.html You can configure it to search only protein families from Pfam to narrow down the search. You'll have to find ORFs before you do this or predict genes (which is harder), ORFs can be found with EMBOSS getorf.