codon family identification
1
0
Entering edit mode
6.4 years ago
Abdullah ▴ 100

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?

biopython • 2.2k views
ADD COMMENT
2
Entering edit mode
6.4 years ago
Siva ★ 1.8k

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

ADD COMMENT
0
Entering edit mode

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

 

 

ADD REPLY
1
Entering edit mode

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

 

ADD REPLY
0
Entering edit mode

thank you very much for the explanation.

 

ADD REPLY

Login before adding your answer.

Traffic: 1837 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6