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:

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.
Have fun!