I would like to have your comments on the following idea:
One often reads in the literature speculations about possible
relationships of proteins with only some 15 to 20% identity scores.
Recently, I thought that a possible method to evaluate the
significance of such low similarity scores would be to randomise the
sequences of these proteins by keeping the relative amino acid
composition. If one does this several times (with one or both of the
sequences), and re-align these randomised sequences with the same gap
creation and gap length weights, in case this original alignment was
significant, the new similarity/identity scores should be
significantly lower. However, if the observed identity is just due to
similar amino acid compositions, the scores should be similar.
1. Does this sound reasonable, and has anybody ever tried a similar
2. Do you know any program that can randomise an amino acid sequence
as described above?
Thanks for your help.
Thorsten Burmester - thorsten at erfurt.thur.de