Next Meeting: Mo, 29.06., 17h, UV10
HMM Based Evolution
The idea is to use Transducers, which act like 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
Papers
Useful Web Ressources
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