Question: TransDecoder in Linux
gravatar for lexa_2294
6 months ago by
lexa_22940 wrote:

Could you help me convert my nucleotide sequences to amino acids in Linux? I already tried putting:

TransDecoder.LongOrfs -t target_transcripts.fasta

but no results. I'm new to bioinformatics and the command terminal.

PS: I already have the TransDecoder program installed

sequence bioinformatic • 270 views
ADD COMMENTlink modified 5 weeks ago by h.mon31k • written 6 months ago by lexa_22940
gravatar for alex.zaccaron
6 months ago by
alex.zaccaron180 wrote:

Looks like you are trying to predict ORFs within assembled transcripts (that is what TransDecoder does). If you successfully ran TransDecoder.LongOrfs -t target_transcripts.fasta, then TransDecoder produces a few files, including longest_orfs.pep which already has the amino acid sequences of the predicted ORFs. But if you just want to translate coding sequences to proteins, use something like EMBOSS transeq.

ADD COMMENTlink modified 6 months ago • written 6 months ago by alex.zaccaron180
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