An introduction to gene prediction

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An introduction to gene prediction
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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

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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

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Signals in Eukaryotes

• Transcription
• Promoter/enhancer/silencer
• TATA box
• Introns/exons
• Donor/acceptor/branch
• polyA
• Repeats
• Alu, Satellites, Expansions
• CpG islands
• Cap/CCAATGC boxes

• Translation
• 5 and 3 UTR
• Kozak consensus
• Start ATG
• Stop TAA/TAG/TGA

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Eukaryotes central dogma
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Promoters/enhancers/silencers
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Intron/exons splicing

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

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Alternative splicing
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Pseudogenes

• Promoters loss, stop codons, frameshifts
• Translocation, duplication

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RNA genes and other problems

• rRNA (ribosome)
• tRNA (transfert)
• snRNA (splicing)
• tmRNA (telomerase)
• Repeats (Alu, satellites, expansion etc)
• CpG islands

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Methods

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

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Programs

• See Lorenzo Cerutti presentation