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Translation reading frames (Read 7971 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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Reply #6 - Apr 9th, 2020 at 6:34pm

Lisa   Offline
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Izwan, i'm glad you asked this question, i had the same problem. Thank you Olga for your answer, it really helped me. However, i have a new question arising this workflow :
If i want to know the % conservation of one peptide (like 8 AA) among all these sequences and not the similarity of entire sequence. How i can do ?
Thank you in advance
 
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Reply #7 - Apr 9th, 2020 at 8:54pm

Olga Golosova   Offline
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Hi Lisa. It's great that you found useful the workflow.

Quote:
If i want to know the % conservation of one peptide (like 8 AA) among all these sequences and not the similarity of entire sequence. How i can do ?

Could you please describe in more detail what you'd like to achieve.

Also, let me give you several recommendations that you might find useful.

1) We added "Search in Alignment" feature in UGENE v.34. You may use it, for example, to find out how many certain peptides are there in your alignment. "Results: 1/8" on the screenshot means that there are 8 results in total and the first one is selected.

Note that you can search in particular columns, if you know the region. Or you can specify if you'd like to do the exact search or use other options.

2) Pay attention to the consensus area. By default, upper-case characters mean all AA in the column are the same. See documentation for details - click the "Help" button on the "General" options panel to open the required documentation page.

3) In case you'd like to get the % similarity of a particular region, extract the region into a new alignment and see the statistics.
 

search-in-alignment.png (218 KB | 124 )
search-in-alignment.png
consensus.png (125 KB | 118 )
consensus.png
similarity.png (225 KB | 110 )
similarity.png
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Reply #8 - Apr 10th, 2020 at 5:10pm

Lisa   Offline
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Hi Ogla,
Thank you for your advices. I want to see % homology/conservation of one peptide among a clade of sequences.
I created a workflow to compared amino acids translation in the reading frame of interest. I did this for 5 sequences for now to make me the hand on ugene but i'll compare more than 4 000 sequences.
After that i want to  see, as you said in 3), see the % similarity in a particular region. The particular region is selected in black on my attachment. How I can extract this region for all sequence into a new alignment ? To have finally something like for example  " the exact peptide is conserved at 80% in the clade". Does it possible on Ugene ?
Thank you in advance,
I hope i'm clear
 
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Reply #9 - Apr 10th, 2020 at 5:35pm

Olga Golosova   Offline
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Hi Lisa,

To extract a region:
-  select it (e.g. if you need to select certain columns, drag your mouse in the corresponding columns in the consensus area)
- choose "Actions > Export > Save subalignment" in the main menu.

To find out % similarity between some reference sequence and other sequences:
- open the "Statistics" options panel tab, as shown on your screenshot, configure the required parameters,
- set a reference sequence (select the sequence and click on the ">" button on the "Statistics" tab).
Thus, the reference sequence will be marked with violet background. Near each sequence name you will see its similarity with the reference one.

To find out the percentage of sequences that have the pattern, you'll need to do some manual calculations:
- search for the pattern and write down the number of results (as in item 1 I described), let's denote it as FOUND_RES
- write down the total number of sequences, let's denote this as SEQUENCES_NUM
Thus, the required percentage number is (FOUND_RES / SEQUENCES_NUM) * 100%

Feel free to ask additional questions, if any.
 
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Reply #10 - Apr 10th, 2020 at 9:09pm

Lisa   Offline
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That was all i need Smiley
Last question to be sure. When you said "as item 1 I described" you speak about "select it (e.g. if you need to select certain columns, drag your mouse in the corresponding columns in the consensus area)" ?
Thank you for your reactivity. It really helped me  Smiley
 
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Reply #11 - Apr 14th, 2020 at 5:44pm

Olga Golosova   Offline
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Quote:
When you said "as item 1 I described" you speak about


I mean this one:
Quote:
1) We added "Search in Alignment" feature in UGENE v.34. You may use it, for example, to find out how many certain peptides are there in your alignment. "Results: 1/8" on the screenshot means that there are 8 results in total and the first one is selected.

Note that you can search in particular columns, if you know the region. Or you can specify if you'd like to do the exact search or use other options.
 
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