Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/30522
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dc.contributor.authorWerner, Johannesen_UK
dc.contributor.authorGéron, Augustinen_UK
dc.contributor.authorKerssemakers, Julesen_UK
dc.contributor.authorMatallana-Surget, Sabineen_UK
dc.date.accessioned2019-12-10T01:05:53Z-
dc.date.available2019-12-10T01:05:53Z-
dc.date.issued2019-12en_UK
dc.identifier.other21en_UK
dc.identifier.urihttp://hdl.handle.net/1893/30522-
dc.description.abstractMetaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue, which is commonly encountered in metaproteomics. mPies’ workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/.en_UK
dc.language.isoenen_UK
dc.publisherSpringer Science and Business Media LLCen_UK
dc.relationWerner J, Géron A, Kerssemakers J & Matallana-Surget S (2019) mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation. Biology Direct, 14 (1), Art. No.: 21. https://doi.org/10.1186/s13062-019-0253-xen_UK
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en_UK
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_UK
dc.subjectBioinformaticsen_UK
dc.subjectMetaproteomicsen_UK
dc.subjectMicrobial ecologyen_UK
dc.subjectProtein annotationen_UK
dc.subjectProtein search databaseen_UK
dc.titlemPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotationen_UK
dc.typeJournal Articleen_UK
dc.identifier.doi10.1186/s13062-019-0253-xen_UK
dc.identifier.pmid31727118en_UK
dc.citation.jtitleBiology Directen_UK
dc.citation.issn1745-6150en_UK
dc.citation.volume14en_UK
dc.citation.issue1en_UK
dc.citation.publicationstatusPublisheden_UK
dc.citation.peerreviewedRefereeden_UK
dc.type.statusVoR - Version of Recorden_UK
dc.contributor.funderRoyal Societyen_UK
dc.citation.date14/11/2019en_UK
dc.contributor.affiliationLeibniz Institute of Baltic Sea Research, Warnemündeen_UK
dc.contributor.affiliationBiological and Environmental Sciencesen_UK
dc.contributor.affiliationGerman Cancer Research Center (DKFZ)en_UK
dc.contributor.affiliationBiological and Environmental Sciencesen_UK
dc.identifier.isiWOS:000497722500001en_UK
dc.identifier.scopusid2-s2.0-85075113804en_UK
dc.identifier.wtid1487756en_UK
dc.contributor.orcid0000-0001-7322-4433en_UK
dc.contributor.orcid0000-0002-6023-3215en_UK
dc.date.accepted2019-10-02en_UK
dc.description.refREF Compliant by Deposit in Stirling's Repositoryen_UK
dc.date.filedepositdate2019-12-09en_UK
dc.relation.funderprojectOCEANCLOCK: Light/dark cycle in picoplankton in response to environmental changeen_UK
dc.relation.funderrefRG160594en_UK
Appears in Collections:Biological and Environmental Sciences Journal Articles

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