PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes.

PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes. J Integr Bioinform. 2016 Oct 01;13(4):16-23 Authors: Has C, Lashin SA, Kochetov A, Allmer J Abstract Improvements in genome sequencing technology increased the availability of full genomes and transcriptomes of many organisms. However, the major benefit of massive parallel sequencing is to better understand the organization and function of genes which then lead to understanding of phenotypes. In order to interpret genomic data with automated gene annotation studies, several tools are currently available. Even though the accuracy of computational gene annotation is increasing, a combination of multiple lines of experimental evidences should be gathered. Mass spectrometry allows the identification and sequencing of proteins as major gene products; and it is only these proteins that conclusively show whether a part of a genome is a coding region or not to result in phenotypes. Therefore, in the field of proteogenomics, the validation of computational methods is done by exploiting mass spectrometric data. As a result, identification of novel protein coding regions, validation of current gene models, and determination of upstream and downstream regions of genes can be achieved. In this paper, we present new functionality for our proteogenomic tool, PGMiner which performs all proteogenomic steps like acquisition of mass spectrometric data, peptide...
Source: Journal of integrative bioinformatics - Category: Bioinformatics Tags: J Integr Bioinform Source Type: research