I have come across a recurrent problem in Jalview, sometimes when I want
to translate a cDNA sequence, Jalview returns an error stating :
"Please select at least three bases in at least one sequences in order
to perform a cDNA translation"
This doesn't happen with all the sequences and when it does, I usually
have more than 3 bases selected in more than one sequence.
Does this have to do with the way I select the sequences or am I missing
something ?
Jalview usually makes this complaint when it cannot create even a single
amino acid from the selected region. Its possible that the error box
also pops up when several sequences are selected, but in one case, there
are less than three bases in the selected region. Can you send me an
example of an alignment where this occurs ? You should be able to
repeat the error by copying the selected region to a new alignment
window, and then trying the 'translate cDNA' option again.
Any help is welcome
we'll see what can be done. The translate cDNA function hasn't been as
thoroughly bugtested as other aspects of the program, so thanks for
querying this.
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/).
Would there be a way of having Jalview translating a cDNA