EstMOI: estimating multiplicity of infection using parasite deep sequencing data.
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ABSTRACT:
SUBMITTER: Assefa SA
PROVIDER: S-EPMC3998131 | biostudies-literature | 2014 May
REPOSITORIES: biostudies-literature
Publications
estMOI: estimating multiplicity of infection using parasite deep sequencing data.
Assefa Samuel A SA Preston Mark D MD Campino Susana S Ocholla Harold H Sutherland Colin J CJ Clark Taane G TG
Bioinformatics (Oxford, England) 20140117 9
Individuals living in endemic areas generally harbour multiple parasite strains. Multiplicity of infection (MOI) can be an indicator of immune status and transmission intensity. It has a potentially confounding effect on a number of population genetic analyses, which often assume isolates are clonal. Polymerase chain reaction-based approaches to estimate MOI can lack sensitivity. For example, in the human malaria parasite Plasmodium falciparum, genotyping of the merozoite surface protein (MSP1/2 ...[more]
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Project description:UnlabelledNew applications of next-generation sequencing technologies use pools of DNA from multiple individuals to estimate population genetic parameters. However, no publicly available tools exist to analyse single-nucleotide polymorphism (SNP) calling results directly for evolutionary parameters important in detecting natural selection, including nucleotide diversity and gene diversity. We have developed SNPGenie to fill this gap. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism type: nonsynonymous, synonymous, or ambiguous. The results allow single nucleotide, single codon, sliding window, whole gene and whole genome/population analyses that aid in the detection of positive and purifying natural selection in the source population.Availability and implementationSNPGenie version 1.2 is a Perl program with no additional dependencies. It is free, open-source, and available for download at https://github.com/hugheslab/snpgenie.Contactnelsoncw@email.sc.edu or austin@biol.sc.eduSupplementary informationSupplementary data are available at Bioinformatics online.
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