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How to do reverse translation? (Read 10694 times)
Oct 23rd, 2012 at 2:22am

Malvolio   Offline
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Hello!

Unipro Ugene is an excellent programme and I really enjoy using it. Unfortunately I couldn't find how to perform reverse translation in GUI mode, although this feature was announced long time ago. Googling "reverse translation" and "back translation" didn't yield anything. Please help!

Thank you!

PS currently I'm using version 1.9.3 from Ubuntu repository, but also have the latest one at hand.
 
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Reply #1 - Oct 23rd, 2012 at 6:46pm

Olga Golosova   Offline
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In the latest UGENE version 1.11.2 to make a reverse complement sequence in the Sequence View, one can use "Edit sequence > Reverse complement sequence" item in the context menu.
 
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Reply #2 - Oct 24th, 2012 at 4:21am

Malvolio   Offline
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Thank you for a rapid reply! But that's not what I meant... Sorry if I didn't state my problem clear enough!
Under reverse or back translation I meant taking a protein sequence and turning it to a nucleotide sequence using known codon usage tables. For this purpose I usually use this programme rev_trans from bioinformatics[dot]org, but it would be nice if I could do it in Ugene interface and the question is if it's possible in current version. Citing the Ugene manpage:

Quote:
The main features of UGENE:

      *      View and analysis of annotated DNA or protein sequences

      *      Chromatograms visualization and editing

      *      Integrated 3D viewer for files in PDB and MMDB formats

      *      Integrated support of search requests to NCBI databases

      *      Multiple sequence alignment using MUSCLE3, MUSCLE4 and KAlign

      *      HMM profiles build and search, based on the source of HMMER2 and
             HMMER3

      *      Modern  protein  secondary structure prediction algorithms based
             on GORIV and PsiPred

      *      Phylogenetic analysis with Phylip

      *      PCR Primers design using Primer3 package

      *      Cloning in silico

      *      Search for transcription factor binding sites in  DNA  sequences
             using SITECON

      *      Search for restriction enzymes and integration with REBASE

      *      Search for direct and invert repeats

      *      DNA reference assembly using Bowtie

      *      Protein back translation

      *      Search for ORFs


Thanks!
 
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Reply #3 - Oct 24th, 2012 at 5:04am

Malvolio   Offline
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By trial and error I figured out how to do back translation in version 1.11.2. Just press "export sequence" for desired amino acid sequence,  check "translate back to nucleic acid alphabet" and select the desired organism. Ugene is great!
 
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