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
Applications and limitations: Ungapped alignments are often used as fast preliminary filters in large-scale sequence searches
See also: Needleman-Wunsch, Smith-Waterman, gapped alignment, BLAST, FASTA.