Generation of ENSEMBL-based proteogenomics databases boost the identification of novel peptides - Mouse dataset

ABSTRACT: A novel bioinformatics tool pypgatk and the pgdb workflow is presented in study 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, notably optimized target/decoy generati on by the algorithm DecoyPyrat.

INSTRUMENT(S): LTQ, Q Exactive HF

ORGANISM(S): Mus Musculus (mouse)

DISEASE(S): Melanoma

SUBMITTER: Yasset Perez-Riverol  

LAB HEAD: Yasset Perez-Riverol

PROVIDER: PXD029362 | Pride | 2021-10-26

REPOSITORIES: pride