[Jalview-discuss] annotation for nucleotide alignments

[Jim Procter]

Dear Stephanie.

Good to hear the issue is cleared up!

On 22/03/2010 10:44, Stephanie Blandin wrote:
>
> Excellent, and sorry I did not think of that earlier...
its understandable. This information is buried in the documentation, and 
that seems to be the problem !
> This time, I also enabled the "consensus" option, so the consensus
> appeared in the annotations and I was able to color the non-conserved
> nucleotides by coloring "by annotation / consensus / below threshold".
> So this solved the problem, and I guess I was doing it like that
> previously, as it did not work either when I tried to color the aln by
> conservation using the previous version of Jalview. I will make a note
> of it, not to forget the trick again ;-)
Hopefully, there will be more default preferences in the future so you 
can simply set the default to 'colour not 100% conserved regions'  - I'm 
thinking this will be something like an 'alignment visualization 
stylesheet' that you can configure yourself.
> Actually, I must also confess I tried to trick the program by
> including amino acid letters at the beginning of the sequences (by the
> way, is there a way to declare it is a nucleotide or an amino acid
> alignment?), but it did not work either, Jalview still considered my
> sequences as nucleotides, and ignored the few aa at the beginning of
> the sequences...
jalview picks the type by working out the proportion of ACTGU symbols in 
the alignment - we did consider allowing the type to be changed, but it 
wasn't really a priority to implement it. I'm sure it'll happen at some 
point, but the more interesting things would be to make it nicer to work 
with nucleic acid sequecnes in Jalview - so - for instance - extending 
the conservation analysis so it calculates conservation for the 
predicted codon translation at each position in a nucleotide alignment, 
rather than simply disabling it.
> I'm happy to send you the aln if you still want to have a look at it,
> just let me know.
>
>  Thanks very much for your help!
>
a pleasure... Happy Jalviewing!
Jim.

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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
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