Sequenceline

Sequenceline is a term used in genomics informatics and data visualization to denote a linear representation of an ordered sequence of elements, typically nucleotides or sequence-derived features, displayed or processed along a coordinate axis such as a reference genome. In visualization contexts, a sequenceline provides a scalable, continuous track where positions are mapped to base pairs or features, enabling inspection of sequence content, spacing, and context for accompanying data such as reads, variants, or annotations. In software tooling, sequenceline can also refer to a data structure that stores a sequence as an ordered collection of nodes or records, each corresponding to a position in the sequence and linked to its neighbors. This abstraction supports traversal, slicing, insertion of new elements, and alignment of external data onto a reference sequence.

Applications include browsing genomic regions, comparing assemblies, and annotating functional elements. Sequencelines are commonly integrated into genome browsers and visualization tools as part of a sequence or coordinate track, and they underpin tasks such as mapping read alignments, identifying single-nucleotide polymorphisms, and displaying gene models relative to sequence positions. The term is not universally standardized; some tools use alternative labels such as "sequence track" or simply "sequence." As with any coordinate-based representation, careful handling of coordinate systems, strand orientation, and reference assemblies is essential.

See also: genome browser, sequence alignment, reference genome, data structure, linked list.