Working with Degenerate Codons in BioPython

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7.1 years ago

ckan91 ▴ 40

I'm trying to get a sub-sequence with only 4 fold, 3 fold ,etc degenerate codons. I found this part of the biopython cookbook that has some functions that could do this [link]. However the code keeps referencing an input to the functions just called "table". I haven't been able for the life of me to figure out that sort of table I should be inputting.

Example: degenerated_subseq(seq, x, table): seq is the sequence, x the level of degeneracy. What is table?

Does anyone have any ideas? Thanks for your help!

Chris

biopython • 3.3k views

ADD COMMENT • link 7.1 years ago by ckan91 ▴ 40

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Check this http://biopython.org/DIST/docs/api/Bio.Data.CodonTable-module.html nd this link http://biopython.org/DIST/docs/api/Bio.Data.CodonTable.CodonTable-class.html the codon table is generated from parsing this file ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt enter image description here

ADD REPLY • link 7.1 years ago by friveroll ▴ 60

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Thanks for the reply friveroll. Would you use it this way? degenerated_subseq(seq_string, 4, Bio.Data.CodonTable.standard_dna_table)

I get a key error when I try it that way. "KeyError: <bio.data.codontable.ncbicodontabledna object="" at="" 0x031e06d0=""> "

ADD REPLY • link 7.1 years ago by ckan91 ▴ 40

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