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)
- 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)
- 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
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modified 3.6 years ago
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3.6 years ago by
microbe77 • 30
