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 | ** 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
- Data Set: The Borrelia burgdorferi B31 genome sequences, N=1500 genes
- Identify host-interacting genes and a set of housekeeping genes
- Calculate the Codon Usage Adaptation Index for each gene
- Test if the biases are significantly different between the virulence genes vs the house keeping genes
- Presentation, Report, & Future directions
Essential Computing skills
- Operating System: Linux/Ubuntu
- Programming Languages: BASH, Perl/BioPerl
- Database Language: SQL
- Statistical Language: R
Essential Readings
- Note: I will post some of the PDFs later
- Borrelia burgdorferi & Lyme disease: A Review
- Codon Usage Biases: Wikipedia
- Borrelia gene regulation: A Review
- Identification of Borrelia virulence genes: A genome-wide expression study
Weigang 11:38, 10 May 2013 (EDT)