Category: Lab Notes: Bioinformatics

Learn how UniProt pathway information connects proteins with metabolic, signaling, and biological pathways and how pathway annotations can be interpreted alongside protein function, evidence, domains, structures, and interactions.

Learn how UniProt connects protein sequences and annotations with experimental and predicted structures, including PDB structures, AlphaFold models, domains, active sites, and variants.

Learn about protein structures in the Protein Data Bank (PDB), including primary, secondary, tertiary, and quaternary structures, major protein types, structural methods, biological functions, and scientific applications.

Explore how UniProt stores and organizes protein sequence data, including amino acid sequences, identifiers, sequence features, domains, variants, isoforms, FASTA files, and related sequence resources.

UniProtKB is the central protein knowledgebase of UniProt, providing protein sequences, functional annotations, evidence, identifiers, sequence features, taxonomy, literature, and cross-references. Learn how UniProtKB/Swiss-Prot and UniProtKB/TrEMBL organize reviewed and unreviewed protein information.

Strain-level antimicrobial resistance surveillance uses genomic and metagenomic data to track resistant microbial strains, investigate genetic relatedness, identify resistance determinants, and monitor potential transmission. Learn how whole-genome sequencing, metagenomics, SNP analysis, phylogenetics, genomic clustering, resistance-gene analysis, and One Health approaches support high-resolution AMR surveillance.

Antimicrobial resistance mechanisms allow microorganisms to survive antimicrobial exposure through processes such as drug inactivation, target modification, target protection, reduced permeability, active efflux, metabolic bypass, and genetic mutation. Learn how metagenomic sequencing can identify and investigate these mechanisms across microbial communities.

Plasmid reconstruction recovers and characterizes plasmid DNA from sequencing data. Learn how metagenomic assembly, short- and long-read sequencing, plasmid detection, host association, genomic context, and resistance-gene analysis are used to investigate plasmids and genetic mobility.

Horizontal gene transfer enables microorganisms to acquire genetic material from other organisms outside normal parent-to-offspring inheritance. Learn how conjugation, transformation, transduction, plasmids, transposons, integrons, and other mobile genetic elements contribute to microbial evolution and antimicrobial resistance, and how metagenomics can investigate genetic mobility.

Antimicrobial resistance databases provide reference sequences and annotations for detecting and interpreting resistance genes. Learn about AMR database types, resistance gene resources, database selection, curation, sequence matching, metagenomic applications, and limitations.

Mobile genetic elements are DNA structures that can move within genomes or between microorganisms and can carry antimicrobial resistance, virulence, metabolic, and adaptive genes. Learn about plasmids, transposons, integrons, insertion sequences, genomic islands, bacteriophages, horizontal gene transfer, and metagenomic methods for studying genetic mobility.

One Health antimicrobial resistance recognizes that resistance develops and spreads across interconnected human, animal, food, agricultural, wastewater, and environmental systems. Learn how metagenomics can investigate antimicrobial resistance genes, resistomes, mobile genetic elements, resistance reservoirs, and potential dissemination pathways across these connected ecosystems.

Resistance gene detection identifies genetic determinants associated with antimicrobial resistance in microbial genomes and communities. Learn how metagenomic sequencing, resistance databases, read-based and assembly-based analysis, gene prediction, abundance profiling, and genomic context are used to detect and characterize antimicrobial resistance genes.

Resistome profiling characterizes antimicrobial resistance genes within microbial communities. Learn how resistomes are detected, quantified, compared, and interpreted using metagenomic sequencing, resistance databases, abundance analysis, diversity analysis, statistical methods, and genomic context.

Resistance gene abundance analysis measures the representation of antimicrobial resistance genes within microbial communities. Learn how resistance genes are quantified using metagenomic sequencing, relative and absolute abundance methods, normalization, prevalence analysis, statistical testing, and genomic context.