Might be too late, but this is how to do it! 1. make a six frame peptide library from you genome (all possible peptides), I use 10 aa +, for 4.5M bp bacterium about 0.25M peptides 2. use this as a reference to get all peptides that map to your possible peptides 3. Get a fasta file that contains all the genome nucleotide sequence (this should be one entry fastafile that contains ALL nucleotides 4. make a nucleotide blast database using makeblastdb command from local blast installation 5. align your peptides to the genome database using tblastn: tblastn -query <your peptide="" fasta="" file=""> -db <your genome="" database="" (these="" are="" three="" files,="" just="" use="" name="" without="" extension)="" -out="" <name="" of="" the="" out="" file="" you="" want=""> -outfmt 6 (the -outfmt 6 will give you tabular results) -max_target_seqs <1 or more, use 1> (not sure about this option though double check!) -evalue 0.001 (to eliminate partial alignment)

1. open file in excel and only keep genome name (useually NC_xxxx), start, stop. Save this file as .bed which will be readable in almost all genome browsers (I use IGB)
2. The code that makes six frames is in python. I will paste the code hereunder:

better to find the code here: https://github.com/microbe777/fasta2six_frames

using tools like tBLASTn could be a good starting point where it compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).

You could try Scipio which uses blat to search a query protein sequence against its genome. It outputs the intron/exon boundaries and splice sites.