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Transposon detection and clustering algorithms

  • Bejerano G, Haussler D, Blanchette M.  Into the heart of darkness: large-scale clustering of human non-coding DNA.  Bioinformatics. 2004 Aug 4;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

Topic revision: r23 - 2008-10-09 - IanHolmes

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