Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10029925 | PMC |
| http://dx.doi.org/10.3389/fbinf.2023.1157956 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Stabilizing the retromer complex rescues synaptic dysfunction and endosomal trafficking deficits in an Alzheimer's disease mouse model.
Acta Neuropathol Commun
September 2025
Department of Biomedical and Clinical Sciences and Department of Clinical Pathology, Linköping University, 58185, Linköping, Sweden.
Disruptions in synaptic transmission and plasticity are early hallmarks of Alzheimer's disease (AD). Endosomal trafficking, mediated by the retromer complex, is essential for intracellular protein sorting, including the regulation of amyloid precursor protein (APP) processing. The VPS35 subunit, a key cargo-recognition component of the retromer, has been implicated in neurodegenerative diseases, with mutations such as L625P linked to early-onset AD.
View Article and Find Full Text PDFDysregulated RNA splicing impairs regeneration in alcohol-associated liver disease.
Nat Commun
September 2025
Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA.
Individuals with progressive liver failure risk dying without liver transplantation. However, our understanding of why regenerative responses are disrupted in failing livers is limited. Here, we perform multiomic profiling of healthy and diseased human livers using bulk and single-nucleus RNA- and ATAC-seq.
View Article and Find Full Text PDFLoss-of-function variations in solute carrier family 38 member 6 are associated with essential tremor.
Signal Transduct Target Ther
September 2025
Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
Essential tremor (ET) is a common neurological disease that is characterized by 4-12 Hz kinetic tremors of the upper limbs and high genetic heterogeneity. Although numerous candidate genes and loci have been reported, the etiology of ET remains unclear. A novel ET-related gene was initially identified in a five-generation family via whole-exome sequencing, and other variants were identified in 772 familial ET probands and 640 sporadic individuals via whole-genome sequencing.
View Article and Find Full Text PDFKaempferol Inhibits Ferroptosis in Lung Epithelial Cells in LPS-Induced Acute Lung Injury via m5C Methylation of TFRC.
Biol Pharm Bull
September 2025
Department of Intensive Care Unit, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310007, China.
Ferroptosis is involved in the progression of sepsis-induced acute lung injury (ALI). Kaempferol is a flavonoid compound that can protect against ALI. 5-Methylcytosine (m5C) is involved in the pathogenesis of sepsis.
View Article and Find Full Text PDFDnaA regulates stationary phase-specific expression of a AAA family gene in Caulobacter crescentus.
Genes Genet Syst
September 2025
Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University.
In most eubacteria the initiator protein DnaA triggers chromosomal replication by forming an initiation complex at the origin of replication and also functions as a transcriptional regulator, coordinating gene expression with cell cycle progression. While DnaA-regulated genes are relatively well characterized in exponentially growing cells, its role in gene regulation during stationary phase remains insufficiently explored. Here, using an aquatic bacterium Caulobacter crescentus as a model, we show that C.
View Article and Find Full Text PDF