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AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization

Daniel Langenkämper, Alexander Goesmann, Tim Wilhelm Nattkemper
2014 BMC Bioinformatics  
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

Alongkorn Kurilung, Vincent Perreten, Nuvee Prapasarakul
2021 Frontiers in Microbiology  
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  
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

Robert Greenhalgh, Wannes Dermauw, Joris J Glas, Stephane Rombauts, Nicky Wybouw, Jainy Thomas, Juan M Alba, Ellen J Pritham, Saioa Legarrea, René Feyereisen, Yves Van de Peer, Thomas Van Leeuwen (+2 others)
2020 eLife  
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]

Valentina Galata, Universität Des Saarlandes
2020
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  
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

Mary Droser, Nigel Hughes, Nicole Bonuso, David Bottjer, Doug Eernisse, Robert Gaines, Austin Hendy, David Jacobs, Jess Miller-Camp, Richard Norris, Kaustav Roy, Peter Sadler (+3 others)
2019 PaleoBios  
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  
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  
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

Rolf Egil Haugerud (ed. in chief), Murray Lankester et al. (iss. eds.)
1998 Rangifer  
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  
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

Rebecca Van Acker, Véronique Storme, Geert Goeminne, Bart Ivens, René Custers, Dirk Aerts, Wim Soetaert, John Ralph, Nicholas Santoro, Jean-Charles Leplé, Gilles Pilate, Wout Boerjan
2011 BMC Proceedings  
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

S. Vezzulli, L. Leonardelli, U. Malossini, M. Stefanini, R. Velasco, C. Moser
2014 Acta Horticulturae  
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  
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  
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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