ungapped

Ungapped alignment is a type of pairwise sequence alignment in which gaps (insertions or deletions) are not allowed. In an ungapped alignment, two sequences are aligned by matching or substituting characters only; a match typically contributes a positive score and a mismatch a negative score according to a substitution matrix. Because gaps are disallowed, the alignment proceeds without insertions or deletions, which makes the method faster but less flexible than gapped alignment.

There are two common forms: ungapped local alignment and ungapped global alignment. Ungapped local alignment seeks the best-scoring, gapless segment common to both sequences. Ungapped global alignment attempts to align the entire sequences with no gaps. Both variants can be computed with dynamic programming, adapted to forbid gap openings and extensions. The absence of gaps reduces memory and time requirements, making ungapped methods suitable for rapid screening, initial similarity estimation, and as components of larger heuristics such as seed-and-extend approaches used in database search tools.

Applications and limitations: Ungapped alignments are often used as fast preliminary filters in large-scale sequence searches or as a baseline to estimate similarity before applying more sensitive gapped methods. They are less effective when sequences differ by insertions or deletions, and can yield misleading results if indels are biologically important. While not a substitute for gapped alignment in many analyses, ungapped approaches provide a computationally light option for quick assessments and for certain algorithmic steps in fast search pipelines.

See also: Needleman-Wunsch, Smith-Waterman, gapped alignment, BLAST, FASTA.