 

<file>Next Meeting: Mo, 29.06., 17h, UV10</file>


====== HMM Based Evolution ======
The idea is to use [[http://biowiki.org/StringTransducers|Transducers]], which act like [[http://biowiki.org/GeneralizedPairHMM|pairHMM]] for simulating evolutionary events. Those Transducers should be based on grammars, so there also a need for a specific grammar and its parser. 


===== Responsibilities =====

|**Subject**|**Name**|
| [[:Teaching:2009summer:RoseP:HMMEvolution:Annotationclass|Annotationclass ''A*****'']] | Kai |
| [[:Teaching:2009summer:RoseP:HMMEvolution:Operations|Operations]] | Madis, Kai |
| [[:Teaching:2009summer:RoseP:HMMEvolution:TransducerModel|Transducer Model]] | Daniel |
| [[:Teaching:2009summer:RoseP:HMMEvolution:TransducerLanguageParser|Transducer Language + Parser]] | Madis |
| [[:Teaching:2009summer:RoseP:HMMEvolution:TransducerSequencer|Transducer Sequencer]] |  |
| [[:Teaching:2009summer:RoseP:HMMEvolution:AnnotationHierarchy|Annotation hierarchy]] | Kai |
| [[:Teaching:2009summer:RoseP:HMMEvolution:Phylotree|Phylotree]] |  |

===== Papers =====

  * {{ 517Introduction_Transducer.pdf | Introduction to Transducers - Mutation and Alignment }} 
  * {{ 517Evolutionary_HMM.pdf | Evolutionary HMMs represented by different Transducers }} 
  * {{ 517Transducer_Basics.pdf | Basic Information and Ideas for Usage of Transducers }} 


===== Useful Web Ressources =====

  * [[http://www.biowiki.org|http://www.biowiki.org]] 


===== First Ideas =====

  * One //Superannotation // for all possible annotations 
  * User can create new Anootations using the Superannotation 
  * All evolutionary steps will be built from a set of parametririzable basic operations:  
    * Insertion 
    * Deletion 
    * Duplication 
    * Double-Cut-Join 
    * Move (Transposon) 
    * Substitution 

    Transducer is sequence based 
    * Need of neutral state (no event) 
    * Step by step (base by Base) 

    Hierarchical annonations, tree like -- (Chromosome (Gen (Intron, Exon)), Transposon) 


===== Further Bla =====

  * Mutationprobabilities (edges in phylotree (inverse probabilities) must be >= 1) will affect only outgoing edges from Match state 
  * Probabilities will be stored in matrices for each annotation and mutation 
  * Startingposition for Transposon/Satelites will be set automatically 


===== Use Cases =====

  * Automaton Modell definieren √ 
  * Automaton Schnittstellen definieren & implementieren√ 
  * Automaton fuer Character-Basierte Evolution erstellen √/X 
  * Automaton Controller erstellen √/X 
  * Join Automata √ 
  * Import von konkreten Automata erstellen X  
  * Schnittstelle zum User Interface herstellen X  
  * Konkrete Automata fuer verschiedene Annotationen erstellen X  
knapp 50% √ 


===== Final Report =====
Download {{ 517report.pdf | here }}.