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cschlaffner / PoGo

PoGo is a proteogenomic tool which allows mapping of peptides identified through mass spectrometry to a reference genome through provided gene annotation.
http://www.sanger.ac.uk/science/tools/pogo
GNU General Public License v3.0
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Using PoGo for proteogenomic mapping of 3-frame translated proteome #18

Open nattzy94 opened 2 years ago

nattzy94 commented 2 years ago

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 KPFLWETIPPICNSCPCLPFSPPSHPRETGQLGASAPTAGPTGAGGSHPRDVCILHS *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!