Novel putative pathogenic viruses identified in pangolins by mining metagenomic data
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Medical Virology"
DOI: 10.1002/jmv.27564
Abstract: The pangolin is the only scaly mammal in the world and also an important reservoir of pathogenic viruses. Habitat loss and poaching have been shrinking the survival range of pangolins. More information on pangolin virus… read more here.
Keywords: novel putative; belonging genus; pathogenic viruses; putative pathogenic ... See more keywords
Metagenomic data reveal diverse fungal and algal communities associated with the lichen symbiosis
Sign Up to like & getrecommendations! Published in 2020 at "Symbiosis"
DOI: 10.1007/s13199-020-00699-4
Abstract: Lichens have traditionally been considered the symbiotic phenotype from the interactions of a single fungal partner and one or few photosynthetic partners. However, lichen symbioses have been shown to be far more complex and may… read more here.
Keywords: fungal algal; data reveal; reveal diverse; diverse fungal ... 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
VirBot: an RNA viral contig detector for metagenomic data
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad093
Abstract: Abstract Summary Without relying on cultivation, metagenomic sequencing greatly accelerated the novel RNA virus detection. However, it is not trivial to accurately identify RNA viral contigs from a mixture of species. The low content of… read more here.
Keywords: rna viral; rna; rna virus; detector ... See more keywords
STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad302
Abstract: Abstract Motivation As the resolution of metagenomic analysis increases, the evolution of microbial genomes in longitudinal metagenomic data has become a research focus. Some software has been developed for the simulation of complex microbial communities… read more here.
Keywords: evolutionary mutations; longitudinal metagenomic; within strain; term evolutionary ... See more keywords
metaXplor: an interactive viral and microbial metagenomic data manager
Sign Up to like & getrecommendations! Published in 2021 at "GigaScience"
DOI: 10.1093/gigascience/giab001
Abstract: Abstract Background Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and… read more here.
Keywords: microbial metagenomic; metaxplor interactive; interactive viral; metaxplor ... See more keywords
PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures
Sign Up to like & getrecommendations! Published in 2018 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkx1321
Abstract: Abstract Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the… read more here.
Keywords: data using; plasmid sequences; plasflow predicting; sequences metagenomic ... See more keywords
METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses
Sign Up to like & getrecommendations! Published in 2021 at "mSystems"
DOI: 10.1128/msystems.00583-21
Abstract: We developed a novel tool, i.e., METAnnotatorX2, that includes a number of new advanced features for analysis of deep and shallow metagenomic data sets and is accompanied by (regularly updated) customized databases for archaea, bacteria,… read more here.
Keywords: metagenomic data; shallow metagenomic; data sets; deep shallow ... See more keywords
Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota
Sign Up to like & getrecommendations! Published in 2022 at "PLOS ONE"
DOI: 10.1371/journal.pone.0281288
Abstract: Environmental factors affect the growth of microorganisms and therefore alter the composition of microbiota. Correlative analysis of the relationship between metagenomic composition and the environmental gradient can help elucidate key environmental factors and establishment principles… read more here.
Keywords: topology; metagenomic data; microbiota; environmental factors ... See more keywords
MCIC: Automated Identification of Cellulases From Metagenomic Data and Characterization Based on Temperature and pH Dependence
Sign Up to like & getrecommendations! Published in 2020 at "Frontiers in Microbiology"
DOI: 10.3389/fmicb.2020.567863
Abstract: As the availability of high-throughput metagenomic data is increasing, agile and accurate tools are required to analyze and exploit this valuable and plentiful resource. Cellulose-degrading enzymes have various applications, and finding appropriate cellulases for different… read more here.
Keywords: dependence; temperature; mcic; identification ... See more keywords