Shape and solar phase angle effects on the taxonomic classification of asteroids

Abstract Candida albicans is the most commonly reported species causing candidiasis. The taxonomic classification of C. albicans and related lineages is controversial, with Candida africana (syn. C. albicans var. africana) and Candida stellatoidea (syn. C. albicans var. stellatoidea) being considered different species or C. albicans varieties depending on the authors. Moreover, recent genomic analyses have suggested a shared hybrid origin of C. albicans and C. africana, but the potential parental lineages remain unidentified. Although the genomes of C. albicans and C. africana have been extensively studied, the genome of C. stellatoidea has not been sequenced so far. In order to get a better understanding of the evolution of the C. albicans clade, and to assess whether C. stellatoidea could represent one of the unknown C. albicans parental lineages, we sequenced C. stellatoidea type strain (CBS 1905). This genome was compared to that of C. albicans and of the closely related lineage C. africana. Our results show that, similarly to C. africana, C. stellatoidea descends from the same hybrid ancestor as other C. albicans strains and that it has undergone a parallel massive loss of heterozygosity.

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VirusTaxo: Taxonomic classification of virus genome using multi-class hierarchical classification by k-mer enrichment

10.1101/2021.04.29.442004 ◽

2021 ◽

Author(s):

Rajan Saha Raju ◽

Abdullah Al Nahid ◽

Preonath Shuvo ◽

Rashedul Islam

Keyword(s):

Genome Sequence ◽

Rna Viruses ◽

Hierarchical Classification ◽

Classification Problem ◽

Virus Genome ◽

Taxonomic Classification ◽

Dna Viruses ◽

Dna And Rna ◽

Full Length Genome

AbstractTaxonomic classification of viruses is a multi-class hierarchical classification problem, as taxonomic ranks (e.g., order, family and genus) of viruses are hierarchically structured and have multiple classes in each rank. Classification of biological sequences which are hierarchically structured with multiple classes is challenging. Here we developed a machine learning architecture, VirusTaxo, using a multi-class hierarchical classification by k-mer enrichment. VirusTaxo classifies DNA and RNA viruses to their taxonomic ranks using genome sequence. To assign taxonomic ranks, VirusTaxo extracts k-mers from genome sequence and creates bag-of-k-mers for each class in a rank. VirusTaxo uses a top-down hierarchical classification approach and accurately assigns the order, family and genus of a virus from the genome sequence. The average accuracies of VirusTaxo for DNA viruses are 99% (order), 98% (family) and 95% (genus) and for RNA viruses 97% (order), 96% (family) and 82% (genus). VirusTaxo can be used to detect taxonomy of novel viruses using full length genome or contig sequences.AvailabilityOnline version of VirusTaxo is available at https://omics-lab.com/virustaxo/.

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Functional and taxonomic classification of a greenhouse water drain metagenome

Standards in Genomic Sciences ◽

10.1186/s40793-018-0326-y ◽

2018 ◽

Vol 13 (1) ◽

Cited By ~ 1

Author(s):

Gamaliel López-Leal ◽

Fernanda Cornejo-Granados ◽

Juan Manuel Hurtado-Ramírez ◽

Alfredo Mendoza-Vargas ◽

Adrian Ochoa-Leyva

Keyword(s):

Taxonomic Classification ◽

Water Drain

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Classification of Autism in Young Children by Phase Angle Clustering in Magnetoencephalogram Signals

2020 National Conference on Communications (NCC) ◽

10.1109/ncc48643.2020.9056022 ◽

2020 ◽

Author(s):

Kasturi Barik ◽

Katsumi Watanabe ◽

Joydeep Bhattacharya ◽

Goutam Saha

Keyword(s):

Young Children ◽

Phase Angle

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Taxonomic Classification of Medically Important Microorganisms

Pocket Guide to Clinical Microbiology, Third Edition ◽

10.1128/9781555817725.ch1 ◽

2014 ◽

pp. 1-19

Keyword(s):

Taxonomic Classification

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Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT

Genome Biology ◽

10.1186/s13059-019-1817-x ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 26

Author(s):

F. A. Bastiaan von Meijenfeldt ◽

Ksenia Arkhipova ◽

Diego D. Cambuy ◽

Felipe H. Coutinho ◽

Bas E. Dutilh

Keyword(s):

Dna Sequences ◽

De Novo ◽

Taxonomic Classification ◽

Classification Method ◽

Reference Database ◽

Annotation Tool ◽

Multiple Signals

Abstract Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT). Classifications are automatically made at low taxonomic ranks if closely related organisms are present in the reference database and at higher ranks otherwise. The result is a high classification precision even for sequences from considerably unknown organisms.

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ETUDE SUR LA VALEUR DES CRITERES CHIMIQUES PROPOSES PAR LA COMMISSION PEDOLOGIQUE DU CANADA POUR LA CLASSIFICATION TAXONOMIQUE DES SOLS DU QUEBEC

Canadian Journal of Soil Science ◽

10.4141/cjss77-029 ◽

1977 ◽

Vol 57 (3) ◽

pp. 233-247 ◽

Cited By ~ 2

Author(s):

ROGER W. BARIL ◽

THI SEN TRAN

Keyword(s):

Cation Exchange ◽

Soil Ph ◽

Classification System ◽

Cation Exchange Capacity ◽

Exchange Capacity ◽

Taxonomic Classification ◽

Single Test ◽

Ph Dependent ◽

Extractable Al

Correlations were made among chemical criteria used for taxonomic soil classificaton. The compared tests were: oxalate Δ (Fe + Al), pyrophosphate-extractable (Fe + Al), oxalate-extractable Al, pH-dependent cation exchange capacity (ΔCEC), ratios of pyrophosphate-extractable (Fe + Al) over clay or over dithionite-extractable (Fe + Al), and finally soil pH measured in 1 M NaF. Significant correlations were found among various measured parameters. However, no single test was found to be reliable as a single criterion when applied to the taxonomic classification of Quebec soils. The two chemical tests, pyrophosphate-extractable (Fe + Al) and its ratio over clay, combined with morphologic criteria appeared useful for classifying Quebec Podzols. A few soils, which presented discrepancies from chemical criteria were found difficult to classify, thus suggesting the possibility of establishing new sub-groups in the Canadain soil taxonomic classification system.

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