Answers.Body: <p>Note that unlike the reverse (nucleotide sequence to protein sequence), which is uniquely defined given a reading frame, the mapping from protein sequence to nucleotide sequence is not unique (it is not a function in the mathematical sense). The method you use to select which of the many (exponential in input sequence length) possible sequences to output depends critically on what the question is.</p>
  <p>If the goal is to design a synthetic gene that will produce a desired protein, then you need to optimize it for expression in the organism into which the gene will be inserted, subject to the constraint of the encoded amino acid sequence.</p>
  <p>If the goal is to search for nucleotide sequences in one or more genomes that could give rise to a certain polypeptide, there is a much better way than to do reverse translation at all. In particular, most putative protein-coding open reading frames in most sequenced genomes have already been run through forward translation code and the expected amino acid sequence encoded in them can be found in databases. So, this problem is reduced to a substring search in these databases.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-20T03:26:33.717Z
Answers.Text: Very interesting! Thanks. That is what I ended up doing. Matching up FASTA files to get sequences.
Answers.UserDisplayName: user2689782
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Answers.CreationDate: 2020-09-16T05:31:03.153Z
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Answers.UserDisplayName: biohacker
Body: <p>Using Biojava 5, I am trying to convert a sequence of Amino Acids to a Nucleotide sequence. Any idea how to do this?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-14T15:24:35.543Z
Comments.Text: Welcome to SE.bioinformatics. What have you tried so far?
Comments.UserDisplayName: user438383
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Comments.CreationDate: 2020-09-14T16:46:25.580Z
Comments.Text: Just looked in BioJava documentation - I don't think they have anything to do this. There is http://www.bioinformatics.org/sms2/rev_trans.html, but I need to write code for this - so can't use that tool
Comments.UserDisplayName: user2689782
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-14T18:08:13.890Z
Comments.Text: "convert a sequence of Amino Acids to a Nucleotide sequence". Like you've mentioned in a comment, this is called "reverse translation". Avoid the word "convert" as much as you can - it is as generic as a word can get in our context. It doesn't look like BioJava has a reverse translate provision - you might need to write some code yourself.
Comments.UserDisplayName: Ram RS
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Comments.CreationDate: 2020-09-14T20:22:02.550Z
Comments.Text: Does this answer your question? [How to translate amino acid sequences to Nucleotide sequences](https://bioinformatics.stackexchange.com/questions/11345/how-to-translate-amino-acid-sequences-to-nucleotide-sequences)
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-20T03:31:16.087Z
Comments.Text: Thanks Chris for that link. Interesting. I ended up using files from NCBI, that worked.
Comments.UserDisplayName: user2689782
Tags: <phylogenetics>
Title: BioJava - Protein to DNA
ThreadText: # BioJava - Protein to DNA
  
  (Asked by: username_0 on 2020-09-14)
  
  Using Biojava 5, I am trying to convert a sequence of Amino Acids to a Nucleotide sequence. Any idea how to do this?
  
  **Tags:** phylogenetics
  
  > **Comments:**
  > **username_1**: Welcome to SE.bioinformatics. What have you tried so far?  
  > **username_0**: Just looked in BioJava documentation - I don't think they have anything to do this. There is http://www.bioinformatics.org/sms2/rev_trans.html, but I need to write code for this - so can't use that tool  
  > **username_2**: "convert a sequence of Amino Acids to a Nucleotide sequence". Like you've mentioned in a comment, this is called "reverse translation". Avoid the word "convert" as much as you can - it is as generic as a word can get in our context. It doesn't look like BioJava has a reverse translate provision - you might need to write some code yourself.  
  > **username_3**: Does this answer your question? [How to translate amino acid sequences to Nucleotide sequences](https://bioinformatics.stackexchange.com/questions/11345/how-to-translate-amino-acid-sequences-to-nucleotide-sequences)  
  > **username_0**: Thanks Chris for that link. Interesting. I ended up using files from NCBI, that worked.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2020-09-16. Score: 1
  
  Note that unlike the reverse (nucleotide sequence to protein sequence), which is uniquely defined given a reading frame, the mapping from protein sequence to nucleotide sequence is not unique (it is not a function in the mathematical sense). The method you use to select which of the many (exponential in input sequence length) possible sequences to output depends critically on what the question is.
  
  If the goal is to design a synthetic gene that will produce a desired protein, then you need to optimize it for expression in the organism into which the gene will be inserted, subject to the constraint of the encoded amino acid sequence.
  
  If the goal is to search for nucleotide sequences in one or more genomes that could give rise to a certain polypeptide, there is a much better way than to do reverse translation at all. In particular, most putative protein-coding open reading frames in most sequenced genomes have already been run through forward translation code and the expected amino acid sequence encoded in them can be found in databases. So, this problem is reduced to a substring search in these databases.
  
  > **Comments:**
  > **username_0**: Very interesting! Thanks. That is what I ended up doing. Matching up FASTA files to get sequences.  
  
  ---
  
  