genomannotation

Genomannotation, often called genome annotation in English, is the process of attaching biological information to genomic sequences. It involves identifying elements such as genes, coding sequences, exons and introns, as well as regulatory regions and other functional features, and linking them to functional descriptions.

Annotations are typically categorized into structural annotation, which determines the locations and structures of genes and other elements, and functional annotation, which assigns putative functions, biological processes, and cellular components. Noncoding RNAs, regulatory motifs, repetitive elements, and pseudogenes are also described during the annotation process.

Methods used in genomannotation include ab initio gene prediction, homology-based approaches that compare the sequence with related species, and evidence-based methods that incorporate transcriptomic data (for example RNA-seq) and proteomics. Modern workflows combine multiple lines of evidence in annotation pipelines such as MAKER and AUGUSTUS, with results presented in genome browsers and public databases.

Outputs of genomannotation consist of gene models and transcript variants, annotated proteins, functional descriptions, Gene Ontology terms, pathway associations, and annotations for noncoding RNAs and regulatory features. Public resources that host annotated genomes include Ensembl, NCBI RefSeq, and UniProt, along with domain and pathway databases such as InterPro.

Quality assessment relies on metrics and tools like BUSCO for completeness and annotation edit distance to compare predicted models with supporting evidence. Challenges include accurately distinguishing closely spaced genes, annotating alternative splicing and noncoding elements, handling repeats, and mitigating errors in draft assemblies.

Genomannotation underpins research in comparative and functional genomics, medical genetics, and agriculture, providing a map from sequence to biology and enabling downstream analyses that illuminate gene function, evolution, and regulation.