title: A distributed computational search strategy for the identification of diagnostics targets: application to finding aptamer targets for methicillin-resistant staphylococci.
abstract: The rapid and cost-effective identification of bacterial species is crucial, especially for clinical diagnosis and treatment. Peptide aptamers have been shown to be valuable for use as a component of novel, direct detection methods. These small peptides have a number of advantages over antibodies, including greater specificity and longer shelf life. These properties facilitate their use as the detector components of biosensor devices. However, the identification of suitable aptamer targets for particular groups of organisms is challenging. We present a semi-automated processing pipeline for the identification of candidate aptamer targets from whole bacterial genome sequences. The pipeline can be configured to search for protein sequence fragments that uniquely identify a set of strains of interest. The system is also capable of identifying additional organisms that may be of interest due to their possession of protein fragments in common with the initial set. Through the use of Cloud computing technology and distributed databases, our system is capable of scaling with the rapidly growing genome repositories, and consequently of keeping the resulting data sets up-to-date. The system described is also more generically applicable to the discovery of specific targets for other diagnostic approaches such as DNA probes, PCR primers and antibodies.
authors: School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors: Keith
authors: K
authors: Flanagan
authors: Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors: Simon
authors: S
authors: Cockell
authors: Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors: Colin
authors: C
authors: Harwood
authors: School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors: Jennifer
authors: J
authors: Hallinan
authors: Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors: Sirintra
authors: S
authors: Nakjang
authors: School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors: Beth
authors: B
authors: Lawry
authors: School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors: Anil
authors: A
authors: Wipat
mesh_terms: D000465:Algorithms; D001331:Automation; D001426:Bacterial Proteins / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D003195:Computer Communication Networks; D003199:Computer Systems; D004247:DNA / Q000737:chemistry; D000939:Epitopes / Q000737:chemistry; D016680:Genome, Bacterial; D008024:Ligands; D055624:Methicillin-Resistant Staphylococcus aureus / Q000187:drug effects / Q000235:genetics*; D010455:Peptides / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D013203:Staphylococcal Infections / Q000175:diagnosis / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D000939:Epitopes; D008024:Ligands; D010455:Peptides; D012313:RNA; D004247:DNA