JASAT -- J A Sequence Alignment Tool

Start by choosing a pair of sequences to align from the menu below.

For a given pair of sequences, JASAT displays the alignment graph -- a graph showing the possible ways the sequences might be aligned.

In this graph:

• a horizontal line indicates base Y was inserted (I) into the first sequence (or that Y was deleted from the second sequence);
• a vertical line indicates base X was deleted (D) from the first sequence (or that X was inserted into the second sequence);
• a diagonal arc indicates a substitution (S): base X in the first sequence was replaced with base Y in the second sequence;
• a diagonal line indicates that the two bases are the same (S) in the two sequences.

Clicking the Compute Least Cost Alignment button computes and displays:

1. the least cost path through the graph (for the given cost settings),
2. BLAST-like alignment strings corresponding to this path, showing how the sequences were aligned,
3. the edit string, showing the sequence operations (I, D, or S) for transforming the first sequence into the second, and
4. the total cost of that alignment.