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dc.contributor.authorRobson, James
dc.contributor.authorBarker, Daniel
dc.date.accessioned2015-10-14T16:10:00Z
dc.date.available2015-10-14T16:10:00Z
dc.date.issued2015-10-13
dc.identifier.citationRobson , J & Barker , D 2015 , ' Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer ' BMC Research Notes , vol. 8 , 561 . DOI: 10.1186/s13104-015-1476-2en
dc.identifier.issn1756-0500
dc.identifier.otherPURE: 218610472
dc.identifier.otherPURE UUID: 9e5a318d-aac4-4fef-90c0-48655ed5d596
dc.identifier.otherScopus: 84943811337
dc.identifier.urihttp://hdl.handle.net/10023/7651
dc.description.abstractBackground: To demonstrate the bioinformatics capabilities of a low-cost computer, the Raspberry Pi, we present a comparison of the protein-coding gene content of two species in phylum Chlamydiae: Chlamydia trachomatis, a common sexually transmitted infection of humans, and Candidatus Protochlamydia amoebophila, a recently discovered amoebal endosymbiont. Identifying species-specific proteins and differences in protein families could provide insights into the unique phenotypes of the two species. Findings: Using a Raspberry Pi computer, sequence similarity-based protein families were predicted across the two species, Chlamydia trachomatis and Protochlamydia amoebophila, and their members counted. Examples include nine multi-protein families unique to C. trachomatis, 132 multi-protein families unique to P. amoebophila and one family with multiple copies in both. Most families unique to C. trachomatis were polymorphic outer-membrane proteins. Additionally, multiple protein families lacking functional annotation were found. Predicted functional interactions suggest one of these families is involved with the exodeoxyribonuclease V complex. Conclusion: The Raspberry Pi computer is adequate for a comparative genomics project of this scope. The protein families unique to P. amoebophila may provide a basis for investigating the host-endosymbiont interaction. However, additional species should be included; and further laboratory research is required to identify the functions of unknown or putative proteins. Multiple outer membrane proteins were found in C. trachomatis, suggesting importance for host evasion. The tyrosine transport protein family is shared between both species, with four proteins in C. trachomatis and two in P. amoebophila. Shared protein families could provide a starting point for discovery of wide-spectrum drugs against Chlamydiae.en
dc.format.extent6en
dc.language.isoeng
dc.relation.ispartofBMC Research Notesen
dc.rights© 2015 Robson and Barker. This 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
dc.subjectChlamydiaen
dc.subjectProtochlamydiaen
dc.subjectChlamydiaeen
dc.subjectparasiteen
dc.subjectendosymbionten
dc.subjectbioinformaticsen
dc.subjectcomparative genomicsen
dc.subjectprotein familiesen
dc.subjectRaspberry Pien
dc.subjectQH301 Biologyen
dc.subject.lccQH301en
dc.titleComparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computeren
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. School of Biologyen
dc.identifier.doihttps://doi.org/10.1186/s13104-015-1476-2
dc.description.statusPeer revieweden
dc.identifier.urlhttp://www.biomedcentral.com/1756-0500/8/561/additional


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