[Jalview-discuss] cDNA codon alignments

[rquiroga at fcq.unc.edu.ar]

I am having three problems.

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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