The "Chemistree" of Porous Coordination Networks: Taxonomic Classification of Porous Solids to Guide Crystal Engineering Studies.
Sign Up to like & getrecommendations! Published in 2021 at "Small"
DOI: 10.1002/smll.202006351
Abstract: New approaches to gas/vapor storage and purification are urgently needed to address the large energy footprint, cost, and/or risk associated with existing technologies. In this context, new classes of porous physisorbents, exemplified by porous coordination… read more here.
Keywords: taxonomic classification; classification; crystal engineering; coordination networks ... See more keywords
Does the genetic diversity among pubescent white oaks in southern Italy, Sicily and Sardinia islands support the current taxonomic classification?
Sign Up to like & getrecommendations! Published in 2020 at "European Journal of Forest Research"
DOI: 10.1007/s10342-020-01334-z
Abstract: Molecular diversity analysis of deciduous pubescent oaks was conducted for populations from Calabria, Sicily and Sardinia. The aims of this study were twofold. First, to provide data on the genetic diversity of pubescent oaks from… read more here.
Keywords: taxonomic classification; diversity; genetic diversity; sicily sardinia ... See more keywords
Perspective on taxonomic classification of uncultivated viruses.
Sign Up to like & getrecommendations! Published in 2021 at "Current opinion in virology"
DOI: 10.1016/j.coviro.2021.10.011
Abstract: Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on… read more here.
Keywords: taxonomic classification; virology; classification uncultivated; uncultivated viruses ... See more keywords
Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks
Sign Up to like & getrecommendations! Published in 2022 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2122636119
Abstract: Significance The correct assignment of DNA sequences to their origin is an important task. However, only a fraction of all species are available in today’s databases and thus easily assignable. Therefore, we present a method… read more here.
Keywords: classification dna; dna; dna sequences; beyond sequence ... See more keywords
RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac011
Abstract: Abstract With advances in library construction protocols and next-generation sequencing technologies, viral metagenomic sequencing has become the major source for novel virus discovery. Conducting taxonomic classification for metagenomic data is an important means to characterize… read more here.
Keywords: usepackage; classification; taxonomic classification; metagenomic data ... See more keywords
MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac184
Abstract: Abstract Motivation Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. 16S rRNA sequence databases like SILVA, RDP, EzBioCloud and HOMD used in downstream bioinformatic pipelines have… read more here.
Keywords: 16s rrna; gene; taxonomic classification; metasquare ... See more keywords
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools
Sign Up to like & getrecommendations! Published in 2022 at "Microbial Genomics"
DOI: 10.1099/mgen.0.000949
Abstract: In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods… read more here.
Keywords: classification; database; parameter database; database choice ... See more keywords
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets
Sign Up to like & getrecommendations! Published in 2022 at "BMC Bioinformatics"
DOI: 10.1101/2022.01.31.478527
Abstract: Background Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic classification and… read more here.
Keywords: precision; classification; classification profiling; taxonomic classification ... See more keywords
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
Sign Up to like & getrecommendations! Published in 2019 at "Genome Biology"
DOI: 10.1186/s13059-019-1817-x
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… read more here.
Keywords: taxonomic classification; classification; robust taxonomic; classification uncharted ... See more keywords
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2022.814437
Abstract: Metagenomic studies unravel details about the taxonomic composition and the functions performed by microbial communities. As a complete metagenomic analysis requires different tools for different purposes, the selection and setup of these tools remain challenging.… read more here.
Keywords: pipeline; shotgun; taxonomic classification; functional annotation ... See more keywords
Pseudomonas Phage MD8: Genetic Mosaicism and Challenges of Taxonomic Classification of Lambdoid Bacteriophages
Sign Up to like & getrecommendations! Published in 2021 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms221910350
Abstract: Pseudomonas phage MD8 is a temperate phage isolated from the freshwater lake Baikal. The organisation of the MD8 genome resembles the genomes of lambdoid bacteriophages. However, MD8 gene and protein sequences have little in common… read more here.
Keywords: taxonomic classification; phage; pseudomonas phage; phage md8 ... See more keywords