Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer
| Autor: | Robson, James F, Barker, Daniel |
|---|---|
| Jazyk: | angličtina |
| Předmět: |
Exodeoxyribonuclease V
Bioinformatics Raspberry Pi Molecular Sequence Data Short Report Gene Expression Chlamydia trachomatis Chlamydiae Open Reading Frames Bacterial Proteins Microcomputers Protein Interaction Mapping Amino Acid Sequence Chlamydia Medicine(all) Endosymbiont Chlamydiales Sequence Homology Amino Acid Biochemistry Genetics and Molecular Biology(all) Comparative genomics Computational Biology Membrane Proteins Molecular Sequence Annotation Parasite Protein families Protochlamydia Sequence Alignment |
| Zdroj: | BMC Research Notes Robson, J F & 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, no. 561, 561 . https://doi.org/10.1186/s13104-015-1476-2 |
| ISSN: | 1756-0500 |
| DOI: | 10.1186/s13104-015-1476-2 |
| Popis: | 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. 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. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1476-2) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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