Borrelia codon usage: Difference between revisions

Revision as of 20:16, 31 July 2013

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 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

Weigang 11:38, 10 May 2013 (EDT)

@@ Line 1: / Line 1: @@
 ==Data==
-[[file:hist 1| 200px]]
+{| class="wikitable"
-[[file:hist 2| 200px]]
+| BBA15 ||  [[file:hist 1| 200px]]
-[[file:hist 3| 200px]]
+|-
-[[file:hist 4| 200px]]
+| BBA24 ||  [[file:hist 2| 200px]]
-[[file:hist 5| 200px]]
+|-
+| BBA68 ||  [[file:hist 3| 200px]]
+|-
+| BBB 18||  [[file:hist 1| 200px]]
+|-
+| Whole genome || [[file:hist 5| 200px]]
+|}
 ==Hypothesis & Background==