TransposonAnnotation < Main

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---++ TransposonAnnotation

__Transposon detection and clustering algorithms__

   * %PMIDC{17932080}%
      * Review of computational methods to study transposable elements in genomes
      * An up-to-date compendium of TE bioinformatics tools from this review can be found [[http://www.bioinf.manchester.ac.uk/bergman/te-tools.html][here]]

   * %PMIDC{16354754}%
      * Transposons are identifiable as big insertions in multi-genome alignments

   * %PMIDC{12176934}%
      * Transposon boundaries correspond to sharp changes in the density of BLAST hits

   * %PMIDC{15262779}%
      * 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

   * %PMIDC{15961452}%
      * Edgar: an "intact instance" of a transposon has multiple BLAST hits sharing exact same coords (i.e. remote homologues that are globally alignable)

   * %PMIDC{15251040}%
      * Nucleotide composition
      * c.f. irreversible substitution models: %PMIDC{17067382}%

   * %PMIDC{16110336}%
      * Combining multiple lines of evidence

   * %PMIDC{16184192}%
      * Transposon prediction directly from shotgun reads

   * %PMIDC{17407597}%
      * LTR transposon identification

__Repeats, copy languages and computational linguistics__

   * %PMIDC{12584121}%
      * Profiling LTR transposons

   * [[http://www.sfb441.uni-tuebingen.de/~lk/TAG-SEMINAR/][Mildly context-sensitive grammar formalisms]] (Kallmeyer, course notes)
      * [[http://citeseer.ist.psu.edu/joshi97treeadjoining.html][Tree-adjoining grammars]] (Joshi and Schabes, 1997)
      * [[http://www.systems.caltech.edu/dsp/students/bjyoon/conf/ssp2005.pdf][Context-sensitive HMMs]] (Yoon and Vaidyanathan)

   * [[http://www.inference.phy.cam.ac.uk/hmw26/crf/][Conditional random fields]] (Hanna Wallach) ([[http://www.inference.phy.cam.ac.uk/hmw26/papers/crf_intro.pdf][PDF]])
      * [[http://www.cis.upenn.edu/~pereira/papers/crf.pdf][Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data]] (Lafferty, !McCallum and Pereira)
      * %PMIDC{16204111}%
      * [[Teaching.AnatCaspiRepetitiveElementSegmentationUsingConditionalRandomFieldsGraduateProject][Repetitive element segmentation]] and [[Teaching.AnatCaspiHomologyAssignmentUsingConditionalRandomFieldsGraduateProject][homology assignment]] (Anat Caspi, 2005)
Topic revision: r23 - 2008-10-09 - IanHolmes