Transcript National Dong Hwa University Genome Sizes

Genome Biology
David Shiuan
Department of Life Science,
Institute of Biotechnology and
Interdisciplinary Program of Bioinformatics
National Dong Hwa University
Genome Sizes
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Pine: 68 billion bp
Corn: 5.0 billion bp
Soybean: 1.1 billion bp
Human: 3.4 billion bp
Housefly: 900 million bp
Rice: 400 million bp
E. coli: 4.6 million bp
HIV: 9.7 thousand bp
http://www.cbs.dtu.dk/databases/DOGS/abbr_table.txt
How Big Is 3.4 Billion?
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Human genome is 3.4 B bp
If the bases were written in
standard 10-point type, on a tape
measure......The tape would
stretch for 5,366 MILES!
Identifying a 500 bp sequence in
a genome would be like finding a
section of this tape measure only
4 feet long...
Greatest Breakthroughs
in Human History
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Manhattan Project
~1940/1944
(Nuclear Energy)
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Apollo Project
~1960/1972
(Moon Landing)
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Human Genome Project
(Decoding the Book of Life)
~1990/2003
The Human Genome Project
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A publicly financed international
research effort. Goal : to decipher the
human genetic code and to provide these
data freely and rapidly to the public.
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Draft announced Jun 2000
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Project completed Apr 2003
Director of the Human Genome
Project and the National Human
Genome Research Institute
(NHGRI). He found the gene
responsible for cystic fibrosis,
Huntington's disease,
neurofibromatosis, multiple
endocrine neoplasia type 1, and the
M4 type of adult acute leukemia.
Venter founded The Institute for
Genomic Research mapping the
human genome. At NIH, Venter
learned of a technique for
rapidly identifying all of the
mRNAs present in a cell, and
began to use it to identify
human brain genes.
in 2000
President Clinton's remarks
announcing completion of
the first phase of the project :
"Today we are learning the
language in which God
created life.“
Collins insists that "science
is not threatened by God; it
is enhanced" and "God is
not threatened by science;
He made it all possible."
How the genome sequences
were determined ?
Yeast artificial chromsomes (YACs) and
bacterial artificial chromsomes (BACs)
Can accomodate from 300 – 500 kb of DNA – great for
large genomes
For the human genome and a
standard plasmid
P – 99% or 0.99 confidence
f – 500 kb/4,400,000 kb = 1.14 x 10-4
N = [ln .01]/[ln 0.999886]
= -4.6/-1.14 x 10-4
= 40,350 individuals
A even bigger improvement!
Reeves et al., 1992, Methods Enzymol. 216:584-603
YAC(Yeast
artificial
chromsome)
self-replicating
vector that can be
maintained in yeast
Can accommodate
large insert
DNA Auto-Sequencers
MUMmer: fast alignment of large-scale
DNA and protein sequences
Annotating the Human Genome
Two Tasks:
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correct placement of known genes
into the proper genomic context
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prediction of previously unknown
genes based on the assembled genomic
sequence.
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What are the
bacterial-unique
genes/proteins?
Vaccine
Design ?
Antibiotics
Discoveries ?
Human Proteome Initiative
Sep 2007
Post Genomic Era
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From one gene, one protein
 genome and proteome
From one to one interaction
 cluster of interactions, pathways
and systems (biology)