Abstract:
UNLABELLED:The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has been developed for simple conditionally essential genome discovery experiments in bacteria. Capable of using raw sequence data files alongside a FASTA sequence of the reference genome and GFF file, PIMMS will generate a tabulated output of each coding sequence with corresponding mapped insertions accompanied with normalized results enabling streamlined analysis. This allows for a quick assay of the genome to identify conditionally essential genes on a standard desktop computer prioritizing results for further investigation. AVAILABILITY:The PIMMS script, manual and accompanying test data is freely available at https://github.com/ADAC-UoN/PIMMS.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Blanchard AM,Leigh JA,Egan SA,Emes RDdoi
10.3389/fgene.2015.00139subject
Has Abstractpub_date
2015-04-09 00:00:00pages
139issn
1664-8021journal_volume
6pub_type
杂志文章abstract::The prevalence of obesity continues to increase particularly in developed countries. To establish the primary mechanisms involved, relevant animal models which track the developmental pathway to obesity are required. This need is emphasized by the substantial rise in the number of overweight and obese children, of whi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2011.00024
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pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00303
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journal_title:Frontiers in genetics
pub_type: 杂志文章
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2014.00244
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abstract::The primary function of leaves is to provide an interface between plants and their environment for gas exchange, light exposure and thermoregulation. Leaves have, therefore a central contribution to plant fitness by allowing an efficient absorption of sunlight energy through photosynthesis to ensure an optimal growth....
journal_title:Frontiers in genetics
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abstract::Understanding the processes that cause speciation is a key aim of evolutionary biology. Lineages or biomes that exhibit recent and rapid diversification are ideal model systems for determining these processes. Species rich biomes reported to be of relatively recent origin, i.e., since the beginning of the Miocene, inc...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
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journal_title:Frontiers in genetics
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00727
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pub_type: 杂志文章,评审
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更新日期:2018-05-08 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00806
更新日期:2019-09-10 00:00:00
abstract::Autosomal dwarfism (adw) in chickens is a growth deficiency caused by a recessive mutation. Characteristic for adw is an approximately 30% growth reduction with short shank. The adw variant was first recognized in the Cornell K-strain of White Leghorns, but the genetic causal variant remained unknown. To identify the ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00193
更新日期:2018-06-07 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00105
更新日期:2019-02-14 00:00:00
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journal_title:Frontiers in genetics
pub_type:
doi:10.3389/fgene.2019.00206
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journal_title:Frontiers in genetics
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doi:10.3389/fgene.2019.00092
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journal_title:Frontiers in genetics
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doi:10.3389/fgene.2019.01031
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journal_title:Frontiers in genetics
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doi:10.3389/fgene.2020.00117
更新日期:2020-03-06 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00012
更新日期:2019-01-30 00:00:00
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journal_title:Frontiers in genetics
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doi:10.3389/fgene.2019.01122
更新日期:2019-11-14 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00031
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00053
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doi:10.3389/fgene.2020.633455
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abstract::Inference of copy number variation presents a technical challenge because variant callers typically require the copy number of a genome or genomic region to be known a priori. Here we present a method to infer copy number that uses variant call format (VCF) data as input and is implemented in the R package vcfR. This ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00123
更新日期:2018-04-13 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00133
更新日期:2019-03-01 00:00:00
abstract::The Xichuan black-bone chicken, which is a rare local chicken species in China, is an important genetic resource of black-bone chickens. Tyrosine can affect melanin production, but the molecular mechanism underlying tyrosine-induced melanin deposition in Xichuan black-bone chickens is poorly understood. Here, the blac...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00457
更新日期:2019-05-15 00:00:00
abstract:Objective:This study reports a Chinese patient with a Congenital Disorder of Glycosylation (CDG) caused by compound-heterozygous mutations in the Conserved Oligomeric Golgi 5 (COG5) gene and thereby offers concrete evidence for early diagnosis. Methods:The clinical manifestations, the results of laboratory examination...
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doi:10.3389/fgene.2020.00168
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journal_title:Frontiers in genetics
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doi:10.3389/fgene.2018.00264
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doi:10.3389/fgene.2019.00957
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00393
更新日期:2020-04-24 00:00:00