The SeqTile software has the capability to “tile” end sequences of inserts against a Reference Sequence to determine locations from which each insert might have eminated; usually, the Reference Sequence is that of a known bacterium and the inserts have been experimentally extracted from a related strain (the Query Genome) and end sequenced, usually at both ends. Once the tiling has been performed, an number of analyses are available to assess certain properties of the Query Genome. Among these are:

  • Genomic Rearrangement Analysis (what rearrangements have occurred in the Query Genome with respect to the Reference Sequence?)
  • Assembly Rearrangement Analysis (how have contigs in an assembly been misconstructed?)
  • Insert Cluster analysis (what insertions have occurred in the Query Genome?)
  • Coverage Analysis (what percentage of the Reference sequence is unique/repeat, and what is the copy number of each replicons in the cellular state?)
  • Repeat Structure Analysis (what is the repeat structure of the Reference Sequence, and how do the copy numbers of the repeats differ in the Query Genome vs. those in the Reference Sequence?)

Recently, SeqTile has been refurbished to work with short-read data, such as those produced by Illumina, and the power of these techniques have been applied to repeat-rich bacteria, such as Shigella dysenteriae.

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