Multiple Sequence Alignment (MSA) Viewer
Progressive Needleman-Wunsch alignment with affine gap penalties, Clustal consensus notation and FASTA export.
How it works
Sequences are aligned progressively: all pairs are aligned with Needleman-Wunsch global alignment under an affine gap penalty, pairwise distances build a guide tree, and sequences are merged in order of similarity. Conservation is annotated with standard Clustal notation — an asterisk for identical columns, a colon for strongly similar residues, a period for weakly similar ones.
Frequently asked questions
What is the difference between global and local sequence alignment?
Global alignment (Needleman-Wunsch) aligns sequences end to end and is appropriate when sequences are of similar length and expected to be homologous throughout. Local alignment (Smith-Waterman) finds the highest-scoring matching region and ignores the rest, which suits finding a conserved domain inside otherwise unrelated sequences or matching a short query against a long subject.
What do the symbols under a Clustal alignment mean?
An asterisk (*) marks a column where every sequence has the same residue. A colon (:) marks conservation between groups of strongly similar properties, such as the acidic residues aspartate and glutamate. A period (.) marks conservation between groups of weakly similar properties. A blank space means no meaningful conservation at that position.
Method reference
Needleman SB & Wunsch CD (1970) J Mol Biol 48(3):443-453.