Using PGx to map 3-frame translation back to the genome

[nattzy94]

Hi,

I have performed a 3-frame translation of an assembled transcriptome. I have a fasta file containing these sequences with the header containing the transcript id and reading frame followed by the translated sequence with stop codons as asterisks. I have included an example below:

ENST00000456328_(+1)
VNLPSAFSLTSSFCSCVFAVSPRLPVSFPPGLEVTGSCCGLHLQVSDFQQLLACARV
QAEHWSGVFLWRGAMPRVGWAIVHLLAPVVCMLNTTTRHRGKIGGKMSESINFSHNLGQ
CVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAEAGPSGTKGILPACSWTSDTPGTL
SWTRCWPGSEPWWRSKPPLVLPLLLCGSSLLPFPFPRASTTPRSHFSLPFVCPVSPEVGL
FLTGSCTTAWRCALPLLCPLETVFVMGLVCRDPATKVKPRRVWSPECCQDPGTGISARWR
KQGNPEEMVGPGHPDLPRAAPLCGIQSVFHPAWPRARLLTGPLQEAAICPAHLLRSETE
QTHLLLPFL**LKLAALDYSPPSLNLRRSPWPQGPCLGACHLPHLLPESFLQPCSLTCPT
ALPGFLSPWLGASSSKSMAPPSLSTTANSKTSSTPTPAIVPRAIRLSALFLETPCLSL
KPFLWETIPPICNSCPCLPFSPPSHPRETGQLGASAPTAGPTGAGGSH*PRDVCILHS
*RSFIKSTLLVS

I have tried using this fasta file as input to PGx but this fails. Can you advise if it is possible to use PGx to map a 3-frame translated proteome back to the genome and how I may do so?

Thank you!