PROJECTS.md

IME Projects

• Reimplement IME paper
• IMEter improved
• IME in C. elegans and D. melanogaster
• IME in fungi
• IME motif finder
• IME BLAST
• IME conservation

Reimplement IME paper

• Make an IMEter using the exact same procedures as the original paper
• Fiind motifs in high scoring introns

IMEter Improved

• Signal decay models
• Sliding window
• HMM - using stuff from the #algorithm sub-group

IME in C. elegans and D. melanogaster

• Try using same procedures as A. thaliana
• Try different procedures
• Find motifs

IME in fungi

• Download fungal genomes and put them in datacore
• Continue with "the usual" methods

IME motif finder

• Recreate the MEME probability models (OOPS, ZOOPS, ANR)
• Create a better probability model that fits IME signals
• Create an algorithm for finding motifs
  • Gibbs sampling?
  • Genetic algorithm?
  • Enumerative digitalized motifs?

IME BLAST

• USE BLASTN with specialized parameters to find conserved IME signals
• Plants first
• Other things...

IME conservation

• Evolution of IME signals in plants
• Other organisms...