Chase W Nelson1, Louise H Moncla2, Austin L Hughes1. 1. Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA and. 2. Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA.
Abstract
UNLABELLED: New 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 IMPLEMENTATION: SNPGenie 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. CONTACT: nelsoncw@email.sc.edu or austin@biol.sc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
UNLABELLED: New 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 IMPLEMENTATION: SNPGenie 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. CONTACT: nelsoncw@email.sc.edu or austin@biol.sc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Austin L Hughes; Bernice Packer; Robert Welch; Andrew W Bergen; Stephen J Chanock; Meredith Yeager Journal: Proc Natl Acad Sci U S A Date: 2003-12-05 Impact factor: 11.205
Authors: Robert Kofler; Pablo Orozco-terWengel; Nicola De Maio; Ram Vinay Pandey; Viola Nolte; Andreas Futschik; Carolin Kosiol; Christian Schlötterer Journal: PLoS One Date: 2011-01-06 Impact factor: 3.752
Authors: Peter R Wilker; Jorge M Dinis; Gabriel Starrett; Masaki Imai; Masato Hatta; Chase W Nelson; David H O'Connor; Austin L Hughes; Gabriele Neumann; Yoshihiro Kawaoka; Thomas C Friedrich Journal: Nat Commun Date: 2013 Impact factor: 14.919
Authors: Adam L Bailey; Michael Lauck; Ria R Ghai; Chase W Nelson; Katelyn Heimbruch; Austin L Hughes; Tony L Goldberg; Jens H Kuhn; Anna J Jasinska; Nelson B Freimer; Cristian Apetrei; David H O'Connor Journal: J Virol Date: 2016-07-11 Impact factor: 5.103
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Authors: Dane D Gellerup; Alexis J Balgeman; Chase W Nelson; Adam J Ericsen; Matthew Scarlotta; Austin L Hughes; Shelby L O'Connor Journal: J Virol Date: 2015-10-21 Impact factor: 5.103
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