1 / 12

An introduction to gene prediction

An introduction to gene prediction. 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.

avism
Download Presentation

An introduction to gene prediction

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. An introduction to gene prediction

  2. 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 Content

  3. 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 Signals in Prokaryotes

  4. 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 Signals in Eukaryotes

  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

More Related