codon family identification

Question

[Abdullah]

Hi,

I have a list of species and a list of their mitochondrial tRNAs anticodons and I want to identify if the anticodon is a 2 or 4 fold degenerate codon family.

Is there an easy way to do this in biopython?

Answer 1

[Siva]

Have a look at this suggestion which uses Bio.Data.CodonTable. First you do a reverse complement of your tRNA anticodon, find the corresponding amino acid and then list the other codons for the amino acid. The following code taken from the above link prints the total number of codons and the corresponding amino acid for codons ACT and ATT. It prints for both the Standard genetic code (id = 1) and the vertebrate mitochondrial genetic code (id=2).

from Bio.Data.CodonTable import unambiguous_dna_by_id
for table in [unambiguous_dna_by_id[1], unambiguous_dna_by_id[2]]:
  print table.id

  for codon in ["ACT", "ATT"]:
    amino = table.forward_table[codon]
    alt_codons = [k for (k,v) in table.forward_table.iteritems()
    if v==amino]
    print "%s -> %s, %i codons for this amino acid" % (codon,amino, len(alt_codons))

which outputs the following:

1
ACT -> T, 4 codons for this amino acid
ATT -> I, 3 codons for this amino acid
2
ACT -> T, 4 codons for this amino acid
ATT -> I, 2 codons for this amino acid

Also, check this site which lists the reverse encoding of tRNA->mRNA including the wobble-pairs.

http://www.soc-bdr.org/rds/authors/unit_tables_conversions_and_genetic_dictionaries/genetic_code_tables/index_en.html#table4

[Abdullah]

Thanks a lot. But why should I reverse complement my anticodon sequence?

It seems that the this table is missing the code = 24 of Rhabdopleura compacta.

http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG24

[Siva]

I am assuming that you are taking the anticodon from a tRNA sequence. In the sequence databases, both the tRNA and mRNA sequences are provided in the 5'->3' direction. So, a tRNA anticodon will be a reverse complement of mRNA codon (See following example for human mitochondrial phenylalanine tRNA from NCBI). The biopython code I copy pasted above takes only mRNA codon(s). So, you need to do a reverse translation to get the mRNA codon(s).

 gene            577..647
                     /gene="TRNF"
                     /nomenclature="Official Symbol: MT-TF | Name:
                     mitochondrially encoded tRNA phenylalanine
     tRNA            577..647
                     /gene="TRNF"
                     /product="tRNA-Phe"
                     /note="NAR: 1455"
                     /anticodon=(pos:611..613,aa:Phe,seq:gaa)
                     /codon_recognized="UUC"

Regarding missing genetic code 24, it is fairly a new addition and it seems to have been included in the recent version of CodonTable

https://github.com/biopython/biopython/commit/5158296bd37905ad66ee4605e48c5752d7e802a0

[Abdullah]

Thank you very much for the explanation.