Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.

ABSTRACT:

Summary

We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling including optimized target/decoy gen

SUBMITTER: Umer HM 

PROVIDER: S-EPMC8825679 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature