Transposon Annotation

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Transposon Annotation

Transposon detection and clustering algorithms

  • Bejerano et al.: Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics 2004;20 Suppl 1:i40-8.
    • Start with a graph whose nodes are all putative transposons & edges correspond to BLAST matches
    • Apply the following heuristic to break up this graph:
      • Split any node whose set of neighbors can be partitioned into two dissimilar subsets
      • Iterate, reducing graph to a set of densely-connected subgraphs

Repeats, copy languages and computational linguistics