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Sequencing Informatics Gabor T. Marth Department of Biology, Boston College marth@bc.edu BI420 – Introduction to Bioinformatics
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The nuclear genome (chromosomes)
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The genome sequence the primary template on which to outline functional features of our genetic code (genes, regulatory elements, secondary structure, tertiary structure, etc.)
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Completed genomes ~1 Mb ~100 Mb >100 Mb ~3,000 Mb
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Main genome sequencing strategies Clone-based shotgun sequencing Whole-genome shotgun sequencing Human Genome ProjectCelera Genomics, Inc.
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Hierarchical genome sequencing BAC library construction clone mapping shotgun subclone library construction sequencing sequence reconstruction (sequence assembly) Lander et al. Nature 2001
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Clone mapping – “sequence ready” map
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Hierarchical genome sequencing BAC library construction clone mapping shotgun subclone library construction sequencing/read processing sequence reconstruction (sequence assembly) Lander et al. Nature 2001
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Shotgun subclone library construction BAC primary clone cloning vector sequencing vector subclone insert
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Hierarchical genome sequencing BAC library construction clone mapping shotgun subclone library construction sequencing/read processing sequence reconstruction (sequence assembly) Lander et al. Nature 2001
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Sequencing
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Robotic automation Lander et al. Nature 2001
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Base calling GGGCTCAGCTGTATCAGCCACGTGCCTACAACAATCTGCCCCT
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Base calling PHRED base = A Q = 40
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Vector clipping
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Hierarchical genome sequencing BAC library construction clone mapping shotgun subclone library construction sequencing/read processing sequence reconstruction (sequence assembly) Lander et al. Nature 2001
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Sequence assembly PHRAP
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Repetitive DNA may confuse assembly
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Sequence completion (finishing) CONSED, AUTOFINISH gap region of low sequence coverage and/or quality
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New sequencing technologies From familiar ABI traces … … and Solexa reads.… to 454 pyrograms … 100 x 1,000 bp 100 thousand x 100 bp 50 million x 20 bp
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