Biosequences

Biosequences are linear sequences of biological monomers that encode information or determine structure and function in living systems. The most common biosequences are nucleic acid sequences (DNA and RNA) and protein sequences composed of amino acids. They are used to identify genes, infer evolutionary relationships, and predict molecular function.

Biosequences are represented by standard alphabets: A, C, G, T for DNA, with U for RNA, and a 20-letter amino acid code for proteins. File formats include FASTA and FASTQ for raw reads, and GenBank/EMBL/DDBJ for annotated sequences. Modern sequencing technologies (Sanger, next-generation, and third-generation platforms) generate reads that are assembled into longer contigs or complete genomes.

Analyses of biosequences include alignment to detect similarity, motif and domain discovery, and annotation. Phylogenetic inference, homology modeling, and structural predictions further interpret sequences. Common tools include BLAST, multiple sequence alignment programs, and hidden Markov models used in gene finding and function prediction.

Biological sequence databases curate large collections of biosequences, such as GenBank, EMBL, DDBJ, and UniProt for proteins. These resources support research across genomics, proteomics, medicine, and agriculture, enabling tasks from variant discovery to tracing evolutionary history.

The rapid growth of sequencing output presents challenges in storage, curation, and computation, while providing rich data for systems biology and personalized medicine.