[Jalview-discuss] Calculating the percent identity between two sequences

Joel Guenther guenthej at gmail.com
Fri Feb 25 21:08:32 GMT 2011

Hi, all.

I'd like to be able to calculate the percent identity for two sequences in
an alignment. The attached alignment (with several empty columns) contains
two sequences that were pulled from a larger structure-based alignment
generated by Dali. In Jalview, when I select the two sequences and perform a
pairwise alignment calculation (Calculate —> Pairwise Alignments...) the
output (attached) only includes an alignment that contains only 7 columns,
but the two sequences are 204 and 224 aa in length and the structures are
highly conserved throughout.

Why isn't Jalview comparing the sequences along their full length, and can I
force it to do so?

If Jalview won't compare full length sequences, is there another program
that will?

Thanks for you help!


Joel M. Guenther, PhD
Department of Chemistry
Kuriyan Laboratory
University of California, Berkeley
176 Stanley Hall, QB3
Berkeley, CA 94720-3220
tel:  <+15106430166> <+15106430166> <+15106430166>
643 0166
fax:  <+15106432352> <+15106432352> <+15106432352>
643 2352
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Score = 50
Length of alignment = 7
Sequence gi|55670498|pdb|1W0H|A :  1 - 204 (Sequence length = 204)
Sequence gi|90109308|pdb|2F96|A :  1 - 224 (Sequence length = 224)

gi|55670498|pdb|1W0H|A gshxads
                       |    | 
gi|90109308|pdb|2F96|A gwxdddd

Percentage ID = 28.57
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