[Jalview-discuss] Jalview - Failed translation

[James Procter]

Hi - this email follows on from our off-list discussion.
adrien wrote:
> I've actually figured out what the issue is, I was working with
> sequences from public databases and to my big disappointment, one single
> sequence contained 3 undefined nucleotides (so much for the quality
> control)...
> I had to go through the whole sequence to find this out (well, luckily,
> Jalview allows to color nucleotides and N show up in white)
> 
> Now I probably have some more bad quality sequences from EMBL/NCBI to
> look at :( Would there be a way of having Jalview translating a cDNA
> that contains N's ? (e.g. by ignoring the codon). I'm don't want to have
> to add a guessed nucleotide to these sequences :(
I have extended the cDNA translation function in Jalview to translate
codons containing ambiguity codes as 'X'. Jalview will consider the 'X'
to be a gap character for any of its internal analyses, but there may be
some unexpected side effects when you use web services. You can try it
at the jalview development build :
(http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest/).

Jim.