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SIM - Alignment Tool for Protein Sequences

SIM is a program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence [more].
Once the alignment is computed, you can view it using LALNVIEW, a graphical viewer program for pairwise alignments [reference to LANVIEW].
Note: You can use the PBIL server to align nucleic acid sequences with a similar tool.

Enter two sequences:

In each box, please enter one UniProtKB AC/ID (e.g. P05130 or KPC1_DROME) OR one protein sequence in single letter code.


Sequence 1:

Sequence 2:


Number of alignments to be computed:
Gap open penalty:
Gap extension penalty: [documentation]]
Comparison Matrix