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CANADA: align

align (version 1.0)

This program has two related functions: It can calculate pairwise global alignments of a pool of DNA
sequences using the Needleman-Wunsch algorithm, or search for the most stable duplex for each pair
and calculate its Gibbs free energy.

See the manual for a more detailed description of this tool.

Download     

The program: align.exe (288 KB)
Example input files: example_seqs.txt (1 KB) example_seqs_w_IDs.txt (1 KB)

Example

align produces alignments:

3 vs. 2:
5'-ggatc---gcaggatctcagtca-3'
    |||    ||||||| ||    
5'-agataacagcaggatttctt   -3'

8 vs. complement of 8:
5'-gtccttcccgcggtttctac-3'
   ||     ||||||     ||
5'-gtagaaaccgcgggaaggac-3'

or duplex base pairings:

6 vs. 3:
5'-agaccgg-gctcc-gcacctgt-3'
    |||  | | ||| ||     
3'-actga-ctctaggacgctagg -5'

7 vs. complement of 7:
5'-cttcacatacaaa-attaatc-3'
   ||||||||||| | |||||||
3'-gaagtgtatgt-tttaattag-5'

and produces also tables with alignment scores / Gibbs free energies.
last modification: Jun/20/2007

  
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