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Terminology for "amino acid frame"

I'm writing a small script which does the following:

  1. Takes an amino acid sequence (ex. GVGP...) and a nucleotide length k
  2. Represent amino acid sequence as triplets of amino acid residues (ex. GGGVVVGGGPPP...)
  3. Run a sliding window across it with length k (ex. if k=5 we have GGGVV, GGVVV, etc)
  4. Count the number of times each unique sequence from (3) occurs in the entire sequence. Also, count the number of synonymous nucleotide sequences that can code for each.

I'm writing a description of this script. I feel that there should be a more clear and concise way to describe this in a couple sentences, or a term that describes the sequences in (3).

Has it been defined before in literature? If not, is there a concise pseudocode that can describe the process? I'm quite new to writing papers in bioinformatics/CS so forgive me if this is an obvious question.

codon
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updated by Ram Ram • written by bravetang8 • bravetang8

5 answers 

"k-mers which code for the same amino acid"

"synonymous nucleotide sequence"

"synonymous codon fragment"

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written by Siva Siva

It looks like there is no accepted terminology. "synonymous codon fragment" sounds pretty good. Though I will probably need to give a proper detailed definition in my text after all.

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written by bravetang8 • bravetang8

What you're doing looks like a simplified version of k-mer counting used for de novo assemblies. I have one question though - Why?

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written by Ram Ram

This is used as a part of a codon optimization algorithm (for gene synthesis) which uses a sliding window to calculate an objective function. I needed to calculate a k value that allowed for enough "diversity" of codon substitutions to achieve the minimum objective.

Perhaps "k-mers which code for the same amino acid" works? Still seems a bit ambiguous to me so maybe it needs to be explicitly defined.

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updated by Ram Ram • written by bravetang8 • bravetang8

Sounds interesting. k-mers that code for same amino acids is a slightly convoluted term for synonymous codons, no?

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written by Ram Ram

If you meant k-mers that code for the same peptide sequence, perhaps synonymous codon-mers might work :)

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written by Ram Ram

Why not "synonymic translation's k-mer"?

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written by fred.s.kremer fred.s.kremer

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written by prakashhandsome72 • prakashhandsome72

Hi,

Please be more careful with your comments. This comment has been marked as spam. If this is a genuine account and we see another instance of spam, we might have to suspend the user account to protect the site.

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written by Ram Ram

synonymous k-codon?

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written by Damian Kao Damian Kao

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