1. An introduction to gene prediction

2. Content Introduction Prokaryotes Start/stop, operons Eukaryotes Start/stop promoter/polyA Intron/exons/UTR Problems Pseudogenes Alternative splicing RNA genes Repeats/CpG island Methods HMMs Neural networks Compositional bias Syntheny Programs

3. Signals in Prokaryotes Transcription start/stop -35 Region TATA box Translation start/stop ORFs Shine-Delgarno motif Start ATG/GTG Stop TAA/TAG/TGA Stem-loops Operons Few special cases Introns, inteins, slipering

4. Signals in Eukaryotes Transcription Promoter/enhancer/silencer TATA box Introns/exons Donor/acceptor/branch polyA Repeats Alu, Satellites, Expansions CpG islands Cap/CCAAT&GC boxes Translation 5’ and 3’ UTR Kozak consensus Start ATG Stop TAA/TAG/TGA

5. Eukaryotes central dogma

6. Promoters/enhancers/silencers

7. Intron/exons splicing Consensus Donor (A,C)AG/GT(A,G)AGT Acceptor TTTTTNCAG/GCCCCC Branch CT(G,A)A(C,T)

8. Alternative splicing

9. Pseudogenes Promoters loss, stop codons, frameshifts Translocation, duplication

10. RNA genes and other problems rRNA (ribosome) tRNA (transfert) snRNA (splicing) tmRNA (telomerase) Repeats (Alu, satellites, expansion etc…) CpG islands

11. Methods Signals Statistics (compositional bias) HMMs Neural networks Homology/Syntheny

12. Programs See Lorenzo Cerutti presentation