title: Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  Using a Raspberry Pi computer, sequence similarity-based protein families were predicted across the two species, C. trachomatis and P. 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK. jr1214@york.ac.uk.|Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK. jr1214@york.ac.uk.
authors.forename: James F
authors.initials: JF
authors.lastname: Robson
authors.affiliation: School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK. db60@st-andrews.ac.uk.
authors.forename: Daniel
authors.initials: D
authors.lastname: Barker
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002692:Chlamydia trachomatis / Q000235:genetics* / Q000378:metabolism; D002695:Chlamydiales / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000295:instrumentation*; D043211:Exodeoxyribonuclease V / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D008838:Microcomputers; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D025941:Protein Interaction Mapping; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; D043211:Exodeoxyribonuclease V