SIM - Alignment Tool for protein sequences

SIM (References) is a program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence.

Once the alignment is computed, you can view it using LALNVIEW, a graphical viewer program for pairwise alignments [references].

Note: You can use the PBIL server to align nucleic acid sequences with a similar tool.

Please enter two sequences. These sequences may either be specified by their Swiss-Prot/TrEMBL accession numbers (AC), e.g. P05130, or by entry names (ID), e.g. KPC1_DROME, or by pasting your own sequences into the boxes below.

SEQUENCE 1: 
 Swiss-Prot/TrEMBL                AC or ID:  




 User-entered sequence       Sequence Name:  


  Paste your sequence below:

SEQUENCE 2: 

 Swiss-Prot/TrEMBL                AC or ID:  




 User-entered sequence       Sequence Name:  


  Paste your sequence below:
Parameters:
Number of alignments to be computed:
Gap open penalty:
Gap extension penalty: (Note about definition of gap penalties.)
Comparison Matrix