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Pre-genomic era: finding your own clones

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GENOME

CHROMOSOMES

YACsor

BACs (map)

PlasmidSub-clones

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Gridded (arrayed/ordered) library

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18,000 BACs for Drosophila

300,000 BACs for Humans

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STS- Sequence Tagged Site Mapping

STS Probe orPCR product

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Minimal Tiling Path

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Sequence 500-750ntFrom each end

Primer walk

PlasmidsOr M13

Sub-clone into smaller segments and mapOr use primer walking- NOT EFFICIENT

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Sub-clone

End sequences

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Virtual DNA(sequence)Assembly

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2 or 3 libraries ofDifferent size fragments

ShotgunSequencing

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Mates: read-pairs

2kb library of clones

10kb library of clones

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1 2 3 23

GENOME

CHROMOSOMES

YACsor

BACs (map)

PlasmidSub-clonesDon’t map Sequence 500-750nt

Assemble sequence of BAC

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Mates: read-pairs

2kb library of clones

10kb library of clones

150kb library of clones

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C. Elegans 100Mb

Drosophila 120Mb

Human 3,200Mb

Cosmids, YACs ordered

BACs ordered- STS mapping+ fingerprinting

BACs ordered- fingerprinting

Whole Genome shotgun

Whole Genome shotgun