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AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization
2014
BMC Bioinformatics
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Results: In this paper we address the problem of rapid taxonomic assignment with small and adaptive data models (< 5 MB) and present the accelerated k-mer explorer (AKE). ...
The tool is presented to the public as a web application (url: https://ani. cebitec.uni-bielefeld.de/ake/, username: bmc, password: bmcbioinfo). ...
Acknowledgements Data for AMD comparison study except AKE results kindly provided by Kaustubh Patil and Alice McHardy. ...
doi:10.1186/s12859-014-0384-0
pmid:25495116
pmcid:PMC4307196
fatcat:tiltrchcofcgto6snwtybcmzja
Comparative Genomic Analysis and a Novel Set of Missense Mutation of the Leptospira weilii Serogroup Mini From the Urine of Asymptomatic Dogs in Thailand
2021
Frontiers in Microbiology
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with the 17 genomes available for L. weilii. ...
Both plasmids contained genes responsible for stress response that may play important roles in bacterial adaptation during persistence in the kidneys. ...
., and Wishart, D. S. (2005). Circular genome visualization and exploration using CGView. ...
doi:10.3389/fmicb.2021.731937
pmid:34733249
pmcid:PMC8558515
fatcat:n2ii3bhnxrckpaopailwe7emfa
International Conference on Emerging Infectious Diseases 2018 Poster and Oral Presentation Abstracts
2018
Emerging Infectious Diseases
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Both read sets were cleaned and analyzed using Kraken and MIDAS for taxonomic classification, BioNumerics v7.6 for wgMLST and VirulenceFinder, ResFinder, and SerotypeFinder (CGE) for gene comparison. ...
Methods: The success of an SMS tool implemented in 2014 to monitor persons returning from West Africa and who have been exposed to Ebola, has motivated the development of a secure web-based SMS tool for ...
Methods: STELaB is an online and offline application with a web-interface for surveillance data entry, validation, reporting and visualization. ...
doi:10.3201/eid2409.nn2409
fatcat:ba2ez7c45zg2plezo64wusdcqu
Genome streamlining in a minute herbivore that manipulates its host plant
2020
eLife
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We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. ...
At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. ...
Exploring Repetitive DNA 1535 Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable 1536 Elements in Eukaryotic Genomes. ...
doi:10.7554/elife.56689
pmid:33095158
pmcid:PMC7738191
fatcat:e5rrpxvdx5e7xmxseimhuhfuse
Resources for the analysis of bacterial and microbial genomic data with a focus on antibiotic resistance
[article]
2020
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BusyBee Web was developed to provide an automatic binning pipeline using frequencies of k-mers (subsequences of length k) Scientific papers This is a cumulative thesis based on the following published ...
The dataset consisted of WGS data, antibiotic susceptibility profiles and meta-information, along with additional taxonomic characterization of a sample subset. ...
ACKNOWLEDGEMENTS We thank Anna Heintz-Buschart and Patrick May for fruitful discussions on clustering and classification. Linda Wampach is thanked for the creation of the BusyBee Web logo. ...
doi:10.22028/d291-31414
fatcat:j2fwsqsp65aaxkdnvayyrwjw3e
Poster Abstracts
2009
Integrative and Comparative Biology
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The presence of elaborate placental specializations in a generalized viviparous lizard is unexpected, and underscores the need for continued explorations of placental diversity in the numerous clades of ...
To further explore the genetic patterning underlying the diversity of tooth morphologies seen in mammals we looked at early dental development of pigs and dolphins. ...
Personal and institutional web pages may suffer from limited expertise in web page design and information management tools. ...
doi:10.1093/icb/icp003
fatcat:ogzq66svibfcjnht5szojhqk3q
11th North American Paleontological Conference Program with Abstracts
2019
PaleoBios
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The Cretaceous-Paleogene (K/Pg) mass extinction event, roughly 66 million year ago, is a well-known time of taxonomic and ecological change for both terrestrial and marine communities. ...
DERMAL DENTICLE ASSEMBLAGES CAN REFLECT Here, we explore the use of dermal denticles, the small tooth-like scales that cover the bodies of sharks and rays, as a new tool for reconstructing historical shark ...
I resampled the fine (< ¼") material and identified small mammal teeth to the lowest taxonomic unit possible based on morphology. I found approximately 300 small mammal teeth useful for my analyses. ...
doi:10.5070/p9361044177
fatcat:zirzr46mm5b3zmfgcrzr4nc3xu
South African Association of Botanists
2003
South African Journal of Botany
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The International Centre for Ethnomedicine and Drug Development (InterCEDD) Nsukka has developed a method for rapid scientific validation of traditional remedies that integrates proof of safety with clinical ...
This paper focuses on the neuroprotective profile of an Amazonian 'brain tonic' to explore newer paradigms of psychotropic drug action and therapy. ...
The antimicrobial activity and death kinetics of the essential oil and chemical components of the South African endemic, Osmitopsis asteriscoides ...
doi:10.1016/s0254-6299(15)30355-0
fatcat:hmxkjip3vbgqjnzqd7rrznqoea
Award Winners and Abstracts of the 30th Anniversary Symposium of The Protein Society, Baltimore, MD, July 16-19, 2016
2016
Protein Science
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In light of the structure we provide a putative explanation for the greatly compromised physiological activity as well as for the enhanced ROS-generation. ...
dehydrogenase (KGDHc), the pyruvate dehydrogenase and the branched-chain ketoacid dehydrogenase complexes and the glycine cleavage system. ...
The WA20-foldon, as a simple and versatile nano-building block, self-assembled into several oligomeric nanoarchitectures (6-mer, 12-mer, 18-mer, 24-mer) in multiples of 6-mer. ...
doi:10.1002/pro.3026
pmid:27783432
pmcid:PMC5081090
fatcat:c4k7luvl4vczfpol76ycqo4nji
7th North Armerican Caribou Conference, 19-21 August 1996, Thunder Bay, Ontario, Canada
1998
Rangifer
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The 7th North American Caribou Conference was held August 19-21 1996, in Thunder Bay, Ontario, Canada where 136 registrants participated in 3 days of sessions and subsequent field tours. ...
Acknowledgments We are grateful for the help given us thtoughout the study by many OMNR staff, Cree of the Hudson Bay lowland villages and volunteers. We specially thank D. ...
I thank managers of Canadian Wildlife Service and Environment Canada for their support.
Acknowledgement I thank two anonymous reviewers who provided many helpful commenrs. ...
doi:10.7557/2.18.5.1393
fatcat:wfhq5xtrings5gpcmayzxwolj4
ACTRIMS-ECTRIMS MSBoston 2014: Poster Sessions 2
2014
Multiple Sclerosis
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Statistical power (alpha=0.05) for the combined MPRAGE-UCCA data was 0.96 for N=24 while power for the individual sites were 0.71 and 0.67 for N=12 and predicted power at N=24 was 0.96 and 0.95. ...
Due to the higher SNR and CNR afforded at 7T, evaluation of the SC in MS shows a significant improvement in lesion visualization compared to the clinical standard at 3T. ...
and a promising tool for long term monitoring of CMCF. ...
doi:10.1177/1352458514547846
pmid:25205049
pmcid:PMC4244175
fatcat:gj757y4jlvejpnrfw22guoit7m
Science, society and biosafety of a field trial with transgenic biofuel poplars
2011
BMC Proceedings
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The black box surrounds the sampling area for Douglas-fir, while the entire range for loblolly pine was sampled. ...
Recent applications of high-throughput sequencing and genotyping technologies to natural populations of forest Figure 1 (abstract I2) The distribution of Douglas-fir and loblolly pine in North America. ...
The availability of the QMI to rapidly assess the potential risk generated by transgenic plants in characterized ecosystems, is a useful tool to assess the releasing or not of the permission of cultivation ...
doi:10.1186/1753-6561-5-s7-i23
fatcat:ulkxqgdupfdktkhsx2kba7pcn4
ASSESSING THE GENETIC VARIABILITY OF GRAPE CLONES
2014
Acta Horticulturae
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Acknowledgments Research carried out with the financial contribution of the University of Bologna, Italy (STARCHitecture Project). ...
The bands obtained were visually scored using 25, 50 and 100 bp ladder (Invitrogen) by Gene Tools software. ...
This is however much less explored for minor diseases, a-biotic stresses and the majority of quality traits. ...
doi:10.17660/actahortic.2014.1046.48
fatcat:ockmijg55ne7bb46gbthiuewhe
Forty-First Annual Meeting March 2–6, 1997 Ernest N. Morial Convention Center New Orleans, Louisiana
1997
Biophysical Journal
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In the SBLM the critical voltage for imstability, Vj,(k), is k-sensitive. For V I < VJ,(0), the ESM is always stable but the SBLM may be unstable. ...
In the SBLM the minimum critical voltage, V, for instability when k . 0 depends on a membrane's elastic moduli and surface tension. Vs is less than in the ESM and there is limited electrostriction. ...
The recent exponential rise in the number of protein structures submitted to the Protein Data Bank (PDB) increases the need for a rapid, fully-automated method for accurate protein fold classification. ...
doi:10.1016/s0006-3495(97)78735-6
fatcat:fwfbe5dox5hunpzqz2y2qfckwi
APS Abstracts Submitted for Presentation at the 2006 APS Annual Meeting
2006
Phytopathology
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A total RNA isolation method was developed for consistent RT-PCR detection of the virus directly from sweetpotato leaves, avoiding dsRNA extraction. HSP70 amplicons were cloned and sequenced. ...
Results were confirmed by RT-PCR using primer pairs CP1/CP3 and HSP70-A/HSP70-B corresponding to the capsid protein and 'heat shock' protein genes, respectively. ...
genomic databases for the generation of tools for understanding of Community epidemiology in tallgrass prairie K. ...
doi:10.1094/phyto.2006.96.6.s1
pmid:18943394
fatcat:c7odyihjrne6tfkpxzgqisab5i
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