With alignobot you can compare sequences by creating global and local alignments. Alignobot can be found at firstname.lastname@example.org.
Before start an alignment be sure that you have 2 sequences selected in the workspace.
Alignobot finds global alignments using the Needleman/Wunsch Algorithm.
Now click “Send” and Alignobot will calculate your aligment and display it:
The Alignment Robot can also find local alignments using the Smith/Waterman algorithm. As with the global alignment you can either use the default similarity function or specify your own. Again support for transition matrices is still to come. Once you have selected and sent your request, the robot will find the best local alignment of the selected two sequences. There might be more than one of them with the same score. The robot will then display all of them.