Codon-Bias documentation

This Python package provides analysis tools for genomic sequences, focusing on protein coding regions, translation efficiency and synonymous mutations.

Contents

• codonbias package
  • Submodules
  • codonbias.pairwise module
    • CodonUsageFrequency
    • PairwiseScore
      • PairwiseScore.get_matrix()
      • PairwiseScore.get_score()
  • codonbias.scores module
    • CodonAdaptationIndex
    • CodonPairBias
    • EffectiveNumberOfCodons
    • FrequencyOfOptimalCodons
    • NormalizedTranslationalEfficiency
    • RelativeCodonBiasScore
    • RelativeSynonymousCodonUsage
    • ScalarScore
      • ScalarScore.get_score()
    • TrnaAdaptationIndex
    • VectorScore
      • VectorScore.get_vector()
    • WeightScore
      • WeightScore.get_weights()
  • codonbias.stats module
    • BaseCounter
      • BaseCounter.count()
      • BaseCounter.get_table()
    • CodonCounter
      • CodonCounter.count()
      • CodonCounter.get_aa_table()
      • CodonCounter.get_codon_table()
  • codonbias.utils module
    • fetch_GCN_from_GtRNAdb()
    • geomean()
    • mean()
    • process_GtRNAdb_table()
    • reverse_complement()

Indices and tables

• Index

• Module Index

• Search Page