you may consider CN3d even though this could be overkill, it plots
conservation onto the structure very well.
>> Dear Bionetters,
> I am looking for a program that can give me a graphical output of
> sequence analysis. To be more specific:
> I have searched for two domains in a set of protein sequences using
> consensus sequence as the probes. Each of these proteins show different
> levels of similarity/identity to the probe & the position of the
> conserved domain is different. Is there any program that could plot a
> graph/or draw a schematic so as to:
> 1) make the similarities/identities visually cospicuous;
> 2) bring out the positional information about the domains.
>> I tried PlotSimilarity but it plots only a pair of sequences at a time.
> Or is there any way to use the data from PlotSimilarity to feed into
> some other program.
> I appreciate any help or hint in advance.
>> Thanks a lot,
> Hari Iyer