An introduction to gene prediction Content Introduction Prokaryotes

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An introduction to gene prediction

An introduction to gene prediction

Content Introduction Prokaryotes Start/stop, operons Start/stop promoter/poly. A Intron/exons/UTR Problems Pseudogenes Alternative splicing RNA

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

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,

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

Eukaryotes central dogma

Promoters/enhancers/silencers

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)

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

Alternative splicing

Alternative splicing

Pseudogenes Promoters loss, stop codons, frameshifts Translocation, duplication

Pseudogenes Promoters loss, stop codons, frameshifts Translocation, duplication

RNA genes and other problems r. RNA (ribosome) t. RNA (transfert) sn. RNA (splicing)

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

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

Programs See Lorenzo Cerutti presentation

Programs See Lorenzo Cerutti presentation