120 research outputs found
GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens
Current methods struggle to reconstruct and visualise the genomic relationships of ≥100,000 bacterial genomes. GrapeTree facilitates the analyses of allelic profiles from 10,000's of core genomes within a web browser window. GrapeTree implements a novel minimum spanning tree algorithm to reconstruct genetic relationships despite missing data together with a static "GrapeTree Layout" algorithm to render interactive visualisations of large trees. GrapeTree is a stand-along package for investigating Newick trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among >160,000 genomes from bacterial pathogens. The GrapeTree package was released under the GPL v3.0 Licence
GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens
Current methods struggle to reconstruct and visualise the genomic relationships of ≥100,000 bacterial genomes. GrapeTree facilitates the analyses of allelic profiles from 10,000's of core genomes within a web browser window. GrapeTree implements a novel minimum spanning tree algorithm to reconstruct genetic relationships despite missing data together with a static "GrapeTree Layout" algorithm to render interactive visualisations of large trees. GrapeTree is a stand-along package for investigating Newick trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among >160,000 genomes from bacterial pathogens. The GrapeTree package was released under the GPL v3.0 Licence
bold: The Barcode of Life Data System (http://www.barcodinglife.org)
The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects
Large-Scale Neighbor-Joining with NINJA
Abstract Neighbor-joining is a well-established hierarchical clustering algorithm for inferring phylogenies. It begins with observed distances between pairs of sequences, and clustering order depends on a metric related to those distances. The canonical algorithm requires O(n3) time and O(n2) space for n sequences, which precludes application to very large sequence families, e.g. those containing 100,000 sequences. Datasets of this size are available today, and such phylogenies will play an increasingly important role in comparative genomics studies. Recent algorithmic advances have greatly sped up neighbor-joining for inputs of thousands of sequences, but are limited to fewer than 13,000 sequences on a system with 4GB RAM. In this paper, I describe an algorithm that speeds up neighbor-joining by dramatically reducing the number of distance values that are viewed in each iteration of the clustering procedure, while still computing a correct neighbor-joining tree. This algorithm can scale to inputs larger than 100,000 sequences because of external-memory-efficient data structures. A free implementation may by obtained fro
Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects
peer-reviewedLactobacillus rhamnosus has been found in many niches, including human intestine, vagina, mouth and dairy products. To intensively investigate the genomic diversity of this species, draft genomes of 70 L. rhamnosus strains isolated from different Chinese subjects were sequenced and further investigated. The pan-genome of L. rhamnosus was open. And gene-trait matching (GTM) was done to explore the carbohydrate utilization ability and antibiotic resistance, and to establish a pattern of gene existence/absence and growth/absence. There were no significant correlations between genetic diversity of the strains and the age or region of the donors. The current results extend the understanding of L. rhamnosus, which could be used as a reference for subsequent research as well as mining and application of the species
Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches
peer-reviewedLactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal
tract of humans and animals. Although a few genomes of L. ruminis were published, most of
them were animal derived. To explore the genetic diversity and potential niche-specific adaptation
changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from
human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was
performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%,
respectively. Both the origin and the sampling distance of these strains had a great influence on
the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains
had a higher consistency in the utilization of carbon source compared to the animal-derived strains.
L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type
of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system
presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the
high denaturation of spacer number and sequence, although cas1 protein was relatively conservative.
The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and
losses attributed to niche adaptations.Innovative Research Group Project of the National Natural Science Foundation of Chin
The Pedagogical Life of Edible Verge Gardens in Sydney: Urban Agriculture for the Urban Food Imaginary.
Ph.D. Thesis. University of Hawaiʻi at Mānoa 2018
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