Show simple item record Kepler, TB Sample, C Hudak, K Roach, J Haines, A Walsh, A Ramsburg, EA
dc.coverage.spatial England 2011-06-21T17:29:33Z 2010-07-21
dc.identifier 1471-2164-11-444
dc.identifier.citation BMC Genomics, 2010, 11 pp. 444 - ?
dc.description.abstract BACKGROUND: The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans. There are two bat genome projects currently underway, a circumstance that promises to speed the discovery host factors important in the coevolution of bats with their viruses. These genomes, however, are not yet assembled and one of them will provide only low coverage, making the inference of most genes of immunological interest error-prone. Many more wildlife genome projects are underway and intend to provide only shallow coverage. RESULTS: We have developed a statistical method for the assembly of gene families from partial genomes. The method takes full advantage of the quality scores generated by base-calling software, incorporating them into a complete probabilistic error model, to overcome the limitation inherent in the inference of gene family members from partial sequence information. We validated the method by inferring the human IFNA genes from the genome trace archives, and used it to infer 61 type-I interferon genes, and single type-II interferon genes in the bats Pteropus vampyrus and Myotis lucifugus. We confirmed our inferences by direct cloning and sequencing of IFNA, IFNB, IFND, and IFNK in P. vampyrus, and by demonstrating transcription of some of the inferred genes by known interferon-inducing stimuli. CONCLUSION: The statistical trace assembler described here provides a reliable method for extracting information from the many available and forthcoming partial or shallow genome sequencing projects, thereby facilitating the study of a wider variety of organisms with ecological and biomedical significance to humans than would otherwise be possible.
dc.format.extent 444 - ?
dc.language eng
dc.language.iso en_US en_US
dc.relation.ispartof BMC Genomics
dc.relation.isversionof 10.1186/1471-2164-11-444
dc.subject Algorithms
dc.subject Animals
dc.subject Chiroptera
dc.subject Cloning, Molecular
dc.subject Gene Expression Profiling
dc.subject Genome
dc.subject Genomics
dc.subject Humans
dc.subject Interferon Type I
dc.subject Interferon-gamma
dc.subject Male
dc.subject Models, Genetic
dc.subject Phylogeny
dc.subject Reproducibility of Results
dc.subject Sequence Analysis, DNA
dc.subject Sequence Homology, Nucleic Acid
dc.title Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler.
dc.title.alternative en_US
dc.type Journal Article
dc.description.version Version of Record en_US 2010-7-21 en_US
duke.description.endpage 444 en_US
duke.description.issue en_US
duke.description.startpage 444 en_US
duke.description.volume 11 en_US
dc.relation.journal Bmc Genomics en_US
pubs.organisational-group /Duke
pubs.organisational-group /Duke/School of Medicine
pubs.organisational-group /Duke/School of Medicine/Basic Science Departments
pubs.organisational-group /Duke/School of Medicine/Basic Science Departments/Molecular Genetics and Microbiology
pubs.publication-status Published online
pubs.volume 11
dc.identifier.eissn 1471-2164

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