Simply Translation DNA to protein without ORF prediction
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17 months ago
SheelS ▴ 40

Several translation tools are available to convert DNA to protein with ORF prediction, and from -1, -2, -3 to 1, 2, 3 frame.

But my question is, are there any command-line-based tools (e.g. shell script or python) to make translate DNA to protein, simply starting from first nucleotide to the last nucleotide with nothing to predict?

For example,

$ python3 translation.tool.py -i input.fasta -o out.fasta  
$ cat input.fasta
>seq1 
CTG GCC TTA CTT 
>seq2 
CAA CGG
$ cat output.fasta
>seq1 
LALL
>seq2 
QR

Any good tools to share, please?

translation • 428 views
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1
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Where did you find the program? What you want is just the 1st frame prediction. The program should allow you to specify that, if does not, find another that does, like this: http://reverse-complement.com/translate-protein/ROOT/

Another one: https://www.ebi.ac.uk/Tools/services/web_emboss_transeq/toolform.ebi

Command-line tool: http://emboss.sourceforge.net/apps/cvs/emboss/apps/transeq.html

António

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0
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You can do this quite easily with e.g. biopython, but you'll need to be able to specify a translation table.

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