hi, i use UGENE and i find that is a very good help!

now im searching for proteins domains using hmmsearch against the proteome, the fasta/gb file is a list of proteins with the sequence, but what i need is to locate them in the genome, because i am working with domains, i dont think i could have problems with introns/exons. also, the translation of the file is quite possible, but how can i annotate the results of my hmmsearch in the genome??

well, im working looking for kinases involved in resistance genes in cassava, the thing is: i generate an hmm, hmmsearch in the proteome, and then, i want to locate those proteins in the genome
so i need the complete sequences of the hmmsearch result (it gives me only the sequences of the domains)
i had to do hmmsearch from console, output a table, import in a spreadsheet, copy.paste the protein names, search for those protein sequences with a perl script from mothur, and im refining the tblastn parameters
but hmm, i dont know if im doing something wrong, but the output of a hmmsearch made with ugene is the entire proteome!!

thank you in advance