Tools for understanding the sequence, evolution, and function
of the human genome. Jim Kent and the Genome Bioinformatics Group
University of California Santa Cruz
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The Goal Make the human genome understandable by humans.
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Step 1 Sequence the human genome
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Idealized Hierarchical Shotgun Sequencing
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Mapping 300,000 BAC Clones Were Digested and Run on Agarose
Gels Cari Soderlunds FPC and Wash U Pathfinders Made Fingerprint
Map Contigs Genetic and radiation hybrid maps placed contigs on
chromsomes Bob Waterston escaping management
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Sequence and Assembly BAC Clones shotgun sequenced at high
throughput to 4x draft. Assembled with Phil Greens Phrap
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GigAssembler Jim Kent David Haussler (meanwhile Celera working
on whole genome shotgun version)
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The Truth +-?++?+-?--?+-?+-?++?+-?--?+-? Keeping strands
straight is the hard part + light - darkness
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Finishing Sequence Using primers to end of contigs close gaps.
Checking automatic assembly especially near tandem repeats.
Checking in-silico restriction digest of BAC matches actual digest.
Time consuming - 1 year to draft genome, 2 years to finish. Human
finished. Mouse will be finished (currently half finished). Other
genomes may stay at draft stage, though draft stage can be very
good these days.
Finding the Genes Dr. Blat helping a gene find itself.
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SIGLEC7 - a gene with some transcriptional complexity. Sialic
Acid Binding/Ig-like Lectin 7 displayed in UCSC Genome Browser
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Genes: Lines of Evidence Full length human mRNA (the best!)
Protein homology with other species. EST evidence - 1st step for
much mRNA. Evidence from genome/genome alignments HMM based gene
finders
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Transferrin Receptor in UCSC Genome Browser
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Clicking on a known gene brings up a large page of information
on the gene. Transferrin
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Current state of human genome ~99% of human genome sequenced.
Last 1% will still be a challenge. ~85% of human genes located.
Substantial resources are being devoted to last 15%. ~20% of human
genes with any depth of functional annotation. Curation and
integrated database are key to progress.