sequenceannotation

Sequence annotation is the process of attaching biological information to nucleotide or amino acid sequences, making raw sequence data interpretable. It encompasses structural annotation, which identifies features such as protein-coding genes, exons, introns, untranslated regions, regulatory regions, noncoding RNAs, repeats, and variants; and functional annotation, which assigns putative roles, gene names, product descriptions, domains, and pathway associations.

Annotation relies on multiple sources of evidence. Ab initio gene prediction analyzes sequence signals like start and stop codons and splice sites. Homology-based annotation transfers information from well-characterized organisms via sequence similarity. Transcript evidence from RNA-seq and proteomics can refine exon boundaries and confirm expression. Results are stored in standardized feature tables and coordinates.

Common data formats include GFF3, GTF, BED, and GenBank feature tables. Pipelines such as MAKER, BRAKER, and AUGUSTUS produce gene models; functional annotation often uses tools like InterProScan, BLAST, and pathway databases. Public annotation resources include Ensembl, NCBI RefSeq, and GENCODE, which provide reference annotations and versioning for model organisms and across releases.

Applications include genome projects, comparative genomics, and functional genomics studies. Annotation quality depends on genome assembly quality, breadth of evidence, and curation efforts. Challenges include accurately predicting complex genes, alternative splicing, noncoding RNAs, repetitive elements, and pseudogenes. Ongoing efforts emphasize reproducibility, traceability, and community annotation to improve completeness and accuracy.