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Local Alignment

Smith-Waterman Algorithm

Find the best matching region between two sequences. Ideal for detecting conserved domains or motifs.

Sequence 1 FASTA or raw

Sequence 2 FASTA or raw

Matrix

Gap Open

Gap Extend

Finding best matching region...

About Local Alignment

Local alignment (Smith-Waterman) finds the best matching region between sequences, ignoring unrelated flanking regions. Ideal for finding domains, motifs, or comparing sequences of different lengths.

Citations

Smith TF and Waterman MS

Identification of common molecular subsequences

Journal of Molecular Biology 1981

PubMed

Biochemintelli

Local Alignment Tool (www.biochemintelli.com/localalign)

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