An introduction to gene prediction Content Introduction Prokaryotes Slides: 12 Download presentation An introduction to gene prediction Content Introduction Prokaryotes Start/stop, operons Start/stop promoter/poly. A Intron/exons/UTR Problems Pseudogenes Alternative splicing RNA genes Repeats/Cp. G island Methods Eukaryotes HMMs Neural networks Compositional bias Syntheny Programs Signals in Prokaryotes Transcription start/stop Translation start/stop -35 Region TATA box ORFs Shine-Delgarno motif Start ATG/GTG Stop TAA/TAG/TGA Stem-loops Operons Few special cases Introns, inteins, slipering Signals in Eukaryotes Transcription Promoter/enhancer/silencer TATA box Introns/exons poly. A Repeats Donor/acceptor/branch Alu, Satellites, Expansions Cp. G islands Cap/CCAAT&GC boxes Translation 5’ and 3’ UTR Kozak consensus Start ATG Stop TAA/TAG/TGA Eukaryotes central dogma Promoters/enhancers/silencers Intron/exons splicing Consensus Donor Acceptor (A, C)AG/GT(A, G)AGT TTTTTNCAG/GCCCCC Branch CT(G, A)A(C, T) Alternative splicing Pseudogenes Promoters loss, stop codons, frameshifts Translocation, duplication RNA genes and other problems r. RNA (ribosome) t. RNA (transfert) sn. RNA (splicing) tm. RNA (telomerase) Repeats (Alu, satellites, expansion etc…) Cp. G islands Methods Signals Statistics (compositional bias) HMMs Neural networks Homology/Syntheny Programs See Lorenzo Cerutti presentation Gene prediction in prokaryotes and eukaryotesGene regulationProkaryotes vs eukaryotes gene regulationGene by gene test resultsChapter 17 gene expression from gene to proteinWhat is espStatic content vs dynamic contentSingle cell organismsPoltrpProkaryoticTranscription in prokaryotes vs eukaryotesMesosome in bacteriaThe oldest prokaryote is