Borrelia codon usage: Difference between revisions

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* Central Hypothesis: Borrelia host-interacting genes show optimal codon usage
* Central Hypothesis: Borrelia host-interacting genes show optimal codon usage
* Background/Rationale:
* Background/Rationale:
** Borrelia is an obligate, non-free-living parasite of vertebrates. A large number of genes are devoted to invade its hosts and to survival a hostile host environment.
** Borrelia is an obligate, non-free-living parasite of vertebrates. A large number of genes are devoted to host invasion and to survival a hostile host environment.
** Evolutionary theory predicts that highly expressed genes use the most abundant tRNA in the cell, and, as a result, they tend to show strong codon usage biases
** Evolutionary theory predicts that highly expressed genes use the most abundant tRNA in the cell, and, as a result, they tend to show strong codon usage biases
** We expect Borrelia host-interacting, virulence-conferring genes use more optimal codons than housekeeping genes
** We expect Borrelia host-interacting, virulence-conferring genes use more optimal codons than housekeeping genes
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==Data & Overview==
==Data & Overview==
# Data Set: The Borrelia burgdorferi B31 genome sequences, N=1500 genes
# Data Set: The Borrelia burgdorferi B31 genome sequences, N=1500 genes

Revision as of 16:05, 10 May 2013

Hypothesis & Background

  • Central Hypothesis: Borrelia host-interacting genes show optimal codon usage
  • Background/Rationale:
    • Borrelia is an obligate, non-free-living parasite of vertebrates. A large number of genes are devoted to host invasion and to survival a hostile host environment.
    • Evolutionary theory predicts that highly expressed genes use the most abundant tRNA in the cell, and, as a result, they tend to show strong codon usage biases
    • We expect Borrelia host-interacting, virulence-conferring genes use more optimal codons than housekeeping genes

Data & Overview

  1. Data Set: The Borrelia burgdorferi B31 genome sequences, N=1500 genes
  2. Identify host-interacting genes and a set of housekeeping genes
  3. Calculate the Codon Usage Adaptation Index for each gene
  4. Test if the biases are significantly different between the virulence genes vs the house keeping genes
  5. Presentation, Report, & Future directions

Essential Computing skills

  • Operating System: Linux/Ubuntu
  • Programming Languages: BASH, Perl/BioPerl
  • Database Language: SQL
  • Statistical Language: R

Essential Readings

Weigang 11:38, 10 May 2013 (EDT)