Question: Alternative to tblastn in which one can define a custom genetic code
0
gravatar for Charles Plessy
4 months ago by
Charles Plessy2.7k
Japan
Charles Plessy2.7k wrote:

I am studying the mitochondrial genome of a tunicate, and in these animals there are extraordinary variations in terms of gene contents and genetic code compared to other chordates (their parent clade). I am searching whole-genome assembly multi-fasta files with tblastn, but in recent versions it does not seem to be able to use a non-standard genetic code. Does anybody know a good alternative (protein query on DNA database) which lets the user define a custom genetic code?

ADD COMMENTlink modified 4 months ago • written 4 months ago by Charles Plessy2.7k
2
gravatar for Jean-Karim Heriche
4 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

I think tblastn uses genetic codes from the gc.prt file so you could presumably add your custom code there and pass its index to option db_gen_code. You may have to recompile the program though (gc.prt is in the src/c++/objects/seqfeat directory of the source code).

ADD COMMENTlink written 4 months ago by Jean-Karim Heriche21k
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