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Old 02-28-2017, 01:47 PM   #1
HLAgroupLK
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Default converting fasta dna files to protein

Hello,

I have 200 human fasta dna files from a region of chr6. Each sequence is 5,500 bp each. I've combined these fasta files and uploaded them into Clustal Omega to generate multiple sequence alignments and phylogenetic tree.

It worked well, however, I would like to convert these sequences into protein and highlights epitopes present in the sequences. What is the best tool to used for this purpose? What format do I need to select for the output?

Thank you so much for your advice.
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Old 03-02-2017, 09:13 AM   #2
gringer
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I've used transeq from the EMBOSS suite:

https://www.ebi.ac.uk/Tools/st/emboss_transeq/

There's a command-line version as well, as part of the free EMBOSS toolkit that is available in most Linux distributions:

http://emboss.sourceforge.net/download/
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Old 03-02-2017, 09:27 AM   #3
Brian Bushnell
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I've also written a nifty tool for nucleotide -> amino translation, but that does not appear to be the goal in this case. Rather, it appears that there are multiple small sequences in a 5500bp region that need to be translated with correct frames. To do so, you need to know the boundaries of these short peptide-encoding sequences, and ignore the non-coding sequence. I don't know of a tool which does that.
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Old 03-02-2017, 01:28 PM   #4
GenoMax
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Cross-posted: https://www.biostars.org/p/239422/

Has been answered there.
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Old 03-02-2017, 04:05 PM   #5
HLAgroupLK
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So far, I've tried EMBOS Transeq and the run aborted before generating anyting for some reason. I've combined multiple fasta files (size was under 1 MB). It worked when I tried it with a really small fasta file. I'm not sure what the problem is?

I've also tried ExPasy tool and it generated an output on the screen but it's not clear to me how to download the result. Also, my final goal is to import the result into Culstal Omega to do the alignment so the format of the output has to be compatible. Should I stick with ExPasy?

Thanks
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Old 03-02-2017, 04:16 PM   #6
GenoMax
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Quote:
Originally Posted by HLAgroupLK View Post
I've also tried ExPasy tool and it generated an output on the screen but it's not clear to me how to download the result. Also, my final goal is to import the result into Culstal Omega to do the alignment so the format of the output has to be compatible. Should I stick with ExPasy?

Thanks
Option 1: Highlight and copy/paste the result data into a separate text file (I assume result is already in fasta format). Be sure to save the file in text format.

Option 2: Choose "file" --> "Save Page as" from your browser window. Be sure to select format as "text file" for the file being saved.

First option may be cleaner. You can then open the file in MEGA or upload to Clustal Omega.
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