Category: Lab Notes: Bioinformatics

Metagenomic quality control is essential for producing reliable sequencing data for downstream analysis. Learn how raw FASTQ reads are assessed, filtered, trimmed, and checked for contamination, host DNA, sequencing artifacts, and other quality issues before taxonomic, functional, and genomic analysis.

Metagenomic sequencing technologies determine how microbial community DNA is converted into sequence data. Learn about short-read and long-read sequencing, sequencing platforms, read length, accuracy, throughput, sequencing depth, hybrid approaches, and metagenomic applications.

Metagenomic library preparation converts extracted microbial DNA into sequencing-ready libraries. Learn about DNA fragmentation, adapter ligation, indexing, amplification, library quantification, pooling, quality control, and preparation methods for short- and long-read sequencing.

Shotgun metagenomics sequences DNA from across microbial genomes to reveal community composition, genes, metabolic pathways, and functional potential. Explore its workflow, applications, advantages, and limitations.

Metagenomic sequencing enables researchers to study the genetic material of entire microbial communities. Learn about sequencing methods, technologies, data analysis, applications, challenges, and future developments.

Learn how UniProt and Reactome complement each other by connecting individual protein information with biological pathways, molecular reactions, interactions, and cellular processes.

Learn how UniProt and KEGG pathways complement each other by connecting detailed protein information with metabolic reactions, signaling pathways, enzymes, metabolites, and biological systems.

Discover how UniProt connects protein functions with metabolic pathways by linking enzymes, EC numbers, biochemical reactions, substrates, cofactors, biological processes, structures, and pathway resources such as KEGG and Reactome.

Explore how UniProt connects signaling proteins with receptors, kinases, phosphatases, transcription factors, protein interactions, cellular localization, post-translational modifications, and biological pathways.

Explore how UniProt connects proteins through molecular interactions, protein complexes, binding regions, signaling pathways, cellular processes, structural information, experimental evidence, and computational predictions.

Learn how UniProt connects proteins through molecular interactions, protein complexes, binding regions, signaling networks, pathways, structures, and experimental or computational evidence.

Gene trees and species trees describe different aspects of evolutionary history. Learn how they are constructed, why they can differ, and how duplication, gene loss, incomplete lineage sorting, horizontal gene transfer, and other processes influence evolutionary relationships.

Learn the GenBank submission process, including sequence preparation, metadata, annotation, validation, accession numbers, data release, and common submission mistakes.

Learn how UniProt entry names identify protein records, how they differ from accession numbers, and how they relate to protein names, gene names, sequences, and annotations.

Learn how UniProt cross-references connect protein entries with genes, genomes, structures, pathways, protein families, Gene Ontology, literature, and other biological databases.