1. National Dong Hwa University
Genome Biology
David Shiuan
Department of Life Science,
Institute of Biotechnology and Interdisciplinary Program of Bioinformatics
National Dong Hwa University

3. Genome Sizes 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

4. How Big Is 3.4 Billion? 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...

5. Greatest Breakthroughs in Human History
Manhattan Project ~1940/1944
(Nuclear Energy)
Apollo Project ~1960/1972
(Moon Landing)
Human Genome Project ~1990/2003
(Decoding the Book of Life)

6. The Human Genome Project
A publicly financed international research effort. Goal : to decipher the human genetic code and to provide these data freely and rapidly to the public.
Draft announced Jun 2000
Project completed Apr 2003

9. 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.

10. 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."

12. How the genome sequences were determined ?

13. A even bigger improvement!
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 ]
= -4.6/-1.14 x 10-4
= 40,350 individuals
A even bigger improvement!

14. YAC(Yeast artificial chromsome)
Reeves et al., 1992, Methods Enzymol. 216:
YAC(Yeast artificial chromsome)
self-replicating vector that can be maintained in yeast
Can accommodate large insert

15. DNA Auto-Sequencers

16. MUMmer: fast alignment of large-scale DNA and protein sequences

17. Annotating the Human Genome
Two Tasks:
correct placement of known genes into the proper genomic context
prediction of previously unknown genes based on the assembled genomic sequence. 

20. What are the
bacterial-unique
genes/proteins?

21. Vaccine Design ?
Antibiotics
Discoveries ?

22. Human Proteome Initiative Sep 2007

61. Post Genomic Era From one gene, one protein  genome and proteome
From one to one interaction
 cluster of interactions, pathways
and systems (biology)