biopython v1.71.0 Bio.SeqUtils.CodonUsage.CodonAdaptationIndex

A codon adaptation index (CAI) implementation.

Implements the codon adaptation index (CAI) described by Sharp and Li (Nucleic Acids Res. 1987 Feb 11;15(3):1281-95).

NOTE - This implementation does not currently cope with alternative genetic codes: only the synonymous codons in the standard table are considered.

Link to this section Summary

Initialize the class

Calculate the CAI (float) for the provided DNA sequence (string)

Generate a codon usage index from a FASTA file of CDS sequences

Prints out the index used

Sets up an index to be used when calculating CAI for a gene

__init__()

Initialize the class.

cai_for_gene()

Calculate the CAI (float) for the provided DNA sequence (string).

This method uses the Index (either the one you set or the one you generated) and returns the CAI for the DNA sequence.

generate_index()

Generate a codon usage index from a FASTA file of CDS sequences.

Takes a location of a Fasta file containing CDS sequences (which must all have a whole number of codons) and generates a codon usage index.

print_index()

Prints out the index used.

set_cai_index()

Sets up an index to be used when calculating CAI for a gene.

Just pass a dictionary similar to the SharpEcoliIndex in the CodonUsageIndices module.