Borrelia codon usage

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Revision as of 19:04, 26 July 2013 by imported>Rayrah (→‎Hypothesis & Background)
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Data

Data.png


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 surviving the host immune defense.
    • 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
  • Importance: If the hypothesis is supported, it would establish a new computational method to identify host-interacting virulence genes based on genome analysis.

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)