The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.

ABSTRACT: On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry-based proteomics data with genomics and transcriptomics information in proteogenomics studies. proBAM and proBed are adaptations of the well-defined, widely used file formats SAM/BAM and BED, respectively, and both have been extended to meet the specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtools and Bedtools, and several widely used genome browsers, can already be used to manipulate and visualize these formats "out-of-the-box." We also highlight that a number of specific additional softwa

SUBMITTER: Menschaert G 

PROVIDER: S-EPMC5793360 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature