Gapped

Gapped is an adjective describing something that contains gaps, openings, or interruptions rather than being continuous. In everyday language it can refer to physical features with holes or spaces, such as a gapped fence or a gapped smile, though the latter phrase is more commonly described as having spaces between teeth. The term is also widely used in specialized contexts to indicate missing parts in a structure, sequence, or dataset.

In molecular biology and bioinformatics, gapped sequences or gapped alignments are central concepts. When comparing DNA, RNA, or protein sequences, alignment algorithms often introduce gap characters to represent insertions or deletions relative to a reference sequence. These gaps are controlled by penalty schemes, such as affine gap penalties, to balance the cost of starting and extending a gap. Gapped alignments enable more accurate inference of evolutionary relationships and functional similarity. The representation of gaps typically uses a dash or a hyphen in text-based formats like FASTA or Clustal.

In data analysis, gapped data refers to missing values or irregular sampling in time series. Handling gaps is a common preprocessing step and may involve deletion, imputation, or specialized models that can accommodate unevenly spaced observations. In other contexts, 'gapped' may describe structures or designs intentionally leaving openings for ventilation, light, or accessibility.