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

Menschaert, G, Wang, X, Jones, AR, Ghali, F, Fenyo, D, Olexiouk, V, Zhang, B, Deutsch, EW, Ternent, T and Vizcaino, JA (2018) The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. Genome Biology, 19. ISSN 1474-760X

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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 software tools, properly supporting the proteomics information available in these formats, are now available providing functionalities such as file generation, file conversion, and data analysis. All the related documentation, including the detailed file format specifications and example files, are accessible at http://www.psidev.info/probam and at http://www.psidev.info/probed.

Item Type: Article
Uncontrolled Keywords: 05 Environmental Sciences, 06 Biological Sciences, 08 Information and Computing Sciences
Subjects: Q Science > QA Mathematics > QA76 Computer software
Q Science > QH Natural history > QH426 Genetics
Divisions: Computer Science
Publisher: BMC Part of Springer Nature
Related URLs:
Date Deposited: 09 Oct 2019 10:35
Last Modified: 09 Oct 2019 10:45
DOI or Identification number: 10.1186/s13059-017-1377-x
URI: http://researchonline.ljmu.ac.uk/id/eprint/11511

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