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Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
Springer Science and Business Media LLC - Tập 3 Số 1 - 2013
D.J. Edwards, Kathryn E. Holt
Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157
Springer Science and Business Media LLC - Tập 1 - Trang 1-7 - 2011
Nicole S Little, Taylor Quon, Chris Upton
Although the crocodilepox virus (CRV) is currently unclassified, phylogenetic analyses suggest that its closest known relatives are molluscum contagiosum virus (MCV) and the avipox viruses. The CRV genome is approximately 190 kb and contains a large number of unique genes in addition to the set of conserved Chordopoxvirus genes found in all such viruses. Upon sequencing the viral genome, others no... hiện toàn bộ
A systematic search for discriminating sites in the 16S ribosomal RNA gene
Springer Science and Business Media LLC - Tập 4 - Trang 1-9 - 2014
Hilde Vinje, Trygve Almøy, Kristian Hovde Liland, Lars Snipen
The 16S rRNA is by far the most common genomic marker used for prokaryotic classification, and has been used extensively in metagenomic studies over recent years. Along the 16S gene there are regions with more or less variation across the kingdom of bacteria. Nine variable regions have been identified, flanked by more conserved parts of the sequence. It has been stated that the discriminatory powe... hiện toàn bộ
Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions
Springer Science and Business Media LLC - Tập 4 - Trang 1-14 - 2014
Kerensa McElroy, Torsten Thomas, Fabio Luciani
Deep sequencing harnesses the high throughput nature of next generation sequencing technologies to generate population samples, treating information contained in individual reads as meaningful. Here, we review applications of deep sequencing to pathogen evolution. Pioneering deep sequencing studies from the virology literature are discussed, such as whole genome Roche-454 sequencing analyses of th... hiện toàn bộ
Growth comparison of several Escherichia coli strains exposed to various concentrations of lactoferrin using linear spline regression
Springer Science and Business Media LLC - - 2012
Camilla Sekse, Jon Bohlin, Eystein Skjerve, G. Vegarud
Abstract Background We wanted to compare growth differences between 13 Escherichia coli strains exposed to various concentrations of the growth inhibitor lactoferrin in two different types of broth (Syncase and Luria-Bertani (LB)). To carry this out, we present a simple statistical procedure that separates microbial growth curves that are due to natural random perturbations and growth curves that ... hiện toàn bộ
Welcome to Microbial Informatics and Experimentation
Springer Science and Business Media LLC - Tập 1 - Trang 1-1 - 2011
Michael J Wise, Barry L Wanner
Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments
Springer Science and Business Media LLC - Tập 2 - Trang 1-11 - 2012
Manal Helal, Fanrong Kong, Sharon CA Chen, Fei Zhou, Dominic E Dwyer, John Potter, Vitali Sintchenko
Comparative genomics has put additional demands on the assessment of similarity between sequences and their clustering as means for classification. However, defining the optimal number of clusters, cluster density and boundaries for sets of potentially related sequences of genes with variable degrees of polymorphism remains a significant challenge. The aim of this study was to develop a method tha... hiện toàn bộ
Metagenomics - Hướng dẫn từ việc lấy mẫu đến phân tích dữ liệu Dịch bởi AI
Springer Science and Business Media LLC - Tập 2 - Trang 1-12 - 2012
Torsten Thomas, Jack Gilbert, Folker Meyer
Metagenomics áp dụng một loạt công nghệ gen và công cụ tin sinh học để truy cập trực tiếp vào nội dung di truyền của toàn bộ cộng đồng sinh vật. Lĩnh vực metagenomics đã đóng vai trò quan trọng trong việc thúc đẩy tiến bộ đáng kể trong sinh thái vi sinh vật, tiến hóa và sự đa dạng trong 5 đến 10 năm qua, và hiện nay nhiều phòng thí nghiệm nghiên cứu đang tích cực tham gia vào lĩnh vực này. Sự gia ... hiện toàn bộ
#metagenomics #sinh thái vi sinh vật #đa dạng sinh học #công nghệ giải trình tự #phân tích thống kê
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset
Springer Science and Business Media LLC - - 2011
Peter E. Larsen, F. Collart, Dawn Field, Folker Meyer, Kevin P. Keegan, Christopher S. Henry, John W. McGrath, John P. Quinn, Jack A. Gilbert
Where the bugs are: analyzing distributions of bacterial phyla by descriptor keyword search in the nucleotide database
Springer Science and Business Media LLC - Tập 1 - Trang 1-8 - 2011
Andrea Squartini
The associations between bacteria and environment underlie their preferential interactions with given physical or chemical conditions. Microbial ecology aims at extracting conserved patterns of occurrence of bacterial taxa in relation to defined habitats and contexts. In the present report the NCBI nucleotide sequence database is used as dataset to extract information relative to the distribution ... hiện toàn bộ
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