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pXg(Proteome Xross Genome)

Introduction

pXg enables to reliably interpret comprehensive genomic events from de novo peptide sequencing inferred by immunopeptidogenomics.
The main functions are here:

1. Linking de novo peptides to RNA-seq evidence directly so that finding where the peptides are originated from.
   
2. The peptides can be matched to RNA-seq reads by chance. pXg estimates empirical distributions about the probability and retrieves significantly matched counts using p-value.
   
3. Even though the peptides are assigned to certain genomic regions supported by RNA-seq, there are chances that the PSMs are not confident. Those erroneous PSMs are estimated at PSM-level FDR using target-decoy approach.
   
4. Comprehensive genomic events such as protein coding, mutation, noncoding, UTR (untranslated region), alternative splicing, intron, intergenic, and even antisense are printed as a result.