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topics/genome-annotation/tutorials/tnseq/tutorial.md

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+# Introduction
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 In microbiology, identifying links between genotype and phenotype is key to understand bacteria growth and virulence mechanisms, and to identify targets for drugs and vaccines. These analysis are limited by the lack of bacterial genome annotations (*e.g.* 30% of genes for *S. pneumoniae* are of unknown function) and by the fact that genotypes often arose from complex composant interactions.
 
 ## Transposon insertion Sequencing
 
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 Transposon insertion sequencing is a technique used to functionally annotate bacterial genomes. In this technique, the genome is saturated by insertions of transposons. Transposons are highly regulated, discrete DNA segments that can relocate within the genome. They have a large influence on gene expression and can be used to determine the function of genes.
 
 When a transposon inserts itself in a gene, the gene's function will be disrupted, affecting the fitness (growth) of the bacteria. We can then manipulate transposons for use in insertional mutagenesis, *i.e.* creation of mutations of DNA by the addition of transposons. The genomes can be then sequenced to locate the transposon insertion site and the function affected by a transposon insertion can be linked to the disrupted gene.