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Translation reading frames (Read 1313 times)
May 4th, 2017 at 4:24pm

izwan   Offline
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Hi,

Is there a way to select the reading frame in which a nucleotide sequence is translated in UGENE? The gene I'm working on seems to have multiple exons with varied reading frames (as suggested by NCBI BLAST results).

I'm trying to compare multiple samples to identify the effects of mutations, and it would help if I didn't have to pre-process the sequences to accommodate the suggested frame.

Thanks in advance.
 
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Reply #1 - May 4th, 2017 at 4:29pm

Olga Golosova   Offline
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Hi!

What do you mean by selecting the frame? Where would you like to select it?
 
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Reply #2 - May 5th, 2017 at 5:07pm

izwan   Offline
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Hi Olga,

I was referring to the reading frames in which the nucleotide sequences are translated into codons. I was wondering if it was possible to do this in the alignment window, following the "Export Amino Acid Translation" selection. Currently, the export will default to one reading frame, which is the first nucleotide sequence in the entire alignment.

The reason for this is to avoid having to manually translate each sequence, selecting those within the relevant frames, and then repeating the alignment to identify any amino acid mutations.
 
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Reply #3 - May 5th, 2017 at 5:22pm

Olga Golosova   Offline
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I'm not sure I fully understand what you would like to achieve, however here is a couple of ideas that may help you:
1) If you remove one or two columns in the alignment before converting it to the amino acid one you'll shift the reading frame.
2) To get all three reading frames per each sequence you may use the Workflow Designer. Screenshot of the workflow and the result is attached. If you need more details about this solution please write.

translate_sequences_workflow.png
 
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Reply #4 - May 5th, 2017 at 5:29pm

izwan   Offline
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Brilliant! That'll do nicely. Thanks!
 
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Reply #5 - May 5th, 2017 at 5:31pm

Olga Golosova   Offline
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Great! You're welcome!  Smiley
 
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