[Jalview-discuss] rev_complement

[James Procter]

Thanks for posting to the list again, John.

John Taylor wrote:
> (so it didn't arrive). I asked about a toggle translation option in
> addition to the reverse complement.  These are tools I use a lot in
> BioEdit.  They are very handy for research and teaching.  Toggle
I can imagine. I think BioEdit still has a lot of fans out there because 
it's got some really practical features.
> translate allows one to get sequences in the proper reading frame. It
> also allows one to switch to amino acids for alignment and then back so
> you end up with a codon alignment.
Does it preserve the variable sites in the third position from the 
original DNA at the end of all this ?

A few months ago there was a feature request concerning something like 
this, but in that case the idea would be to either have one view which 
showed the codon alignment, and the other would be the corresponding 
protein alignment. Scrolling would be tied between both alignment views, 
so moving the focus in one would also move the other.  I'm afraid that 
kind of manipulation is not yet implemented either, but I'm just trying 
to get an idea of what would be most useful to everyone.

The back-translation function is really the most significant missing 
feature in Jalview at the moment. If the sequence is in Uniprot and has 
an EMBL cross reference then it can retrieve that sequence and propagate 
annotation from the protein back onto it, but not much more. Going from 
DNA to protein is better supported (ie an aligned set of coding regions 
are properly translated to an aligned set of proteins), but for a 
protein alignment there's curently no way of reconstructing the aligned 
cDNA from it. All the basic mechanisms are available to do this, but we 
have to find (someone's) time to actually write the routine to do it.

The reverse complement option is
> also handy. My aim is to convert my lab to Linux. BioEdit is the main
> thing holding us back (it's only available for Windows).
Wine may be the only way forward at the moment :(  perhaps this'll 
change in a few months, though.
> When might we expect Jalview 2.4?
There is a paper being drafted at the moment, and so the official 
release of 2.4 has been delayed until this is complete. However, you can 
get at a webstart version of the application from here:

http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/release/webstart/jalview.jnlp

Jim.