One is the Translation of cDNA, which seems to not handle gaps correctly sometimes,
(ATAAAG---GTTCCT) translates to (IKVP)
(ATAAAA---GTTCCA) translates to (IKVP), missing the gap.
Also I get a "Please select at least three bases in at least one sequence in order to perform a cDNA translation." when I try to translate my entire cDNA codon alignment to protein. (Sequences: 154 Minimum Sequence Length: 314 Maximum Sequence Length: 365 Average Length: 351). Maybe too big?
My third concern is that the translated window that appears has linked highlighting, but it would be great if column selection were also linked between them. In this way one could hide columns in the protein alignment and have the corresponding codons hidden in the codon alignment.
Lastly, is there any way to just give Jalview a protein alignment, and somehow "tell it" that it is the translation of a previously opened cDNA alignment?
Thank you for your time, best regards,
Rodrigo Quiroga
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One is the Translation of cDNA, which seems to not handle gaps
correctly sometimes,
(ATAAAG---GTTCCT) translates to (IKVP)
(ATAAAA---GTTCCA) translates to (IKVP), missing the gap.
The translate cDNA function will exclude any gapped columns from the
translated protein alignment. Otherwise, gaps are introduced when codons
intersect but are misaligned.
e.g.
A-TAAAG
AATAA-G
becomes
-I-K
N-K-
Also I get a "Please select at least three bases in at least one
sequence in order to perform a cDNA translation." when I try to
translate my entire cDNA codon alignment to protein. (Sequences: 154
Minimum Sequence Length: 314 Maximum Sequence Length: 365 Average
Length: 351). Maybe too big?
My guess is that you have one or two Ns in the region you are
translating. The translate cDNA routine complains when the effective
number of *defined* bases that have been selected for translation is not
divisible by three. This is partly because it doesn't know how to use an
N or an X (or ?) in a codon.
My third concern is that the translated window that appears has linked
highlighting, but it would be great if column selection were also
linked between them. In this way one could hide columns in the protein
alignment and have the corresponding codons hidden in the codon
alignment.
This is actually on our TODO list. The development version is now at the
point where selections can be passed across coordinate systems (e.g. DNA
to protein).
Lastly, is there any way to just give Jalview a protein alignment, and
somehow "tell it" that it is the translation of a previously opened
cDNA alignment?
no - this kind of reassociation of imported data with the currently
displayed alignments is also on our TODO list, so there might be a way
in a release or two's time (its possible with the code, but the GUI
hasn't been implemented). I wonder though - are you only wanting to do
this because the cDNA translation has failed ?