Using PoGo for proteogenomic mapping of 3-frame translated proteome #18
Description
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 PoGo 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!