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????????? ??? Human genome project and Computer science

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Title: Human genome project and Computer science Author: Hyung-Yong Kim Last modified by: Hyungyong Kim Created Date – PowerPoint PPT presentation

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Title: ????????? ??? Human genome project and Computer science


1
????????? ??? Human genome project and Computer
science
  • 2005-12-03 Biocom OB ???
  • 93 ???
  • http//biohackers.net/wiki/HgpAndComputer

2
??
  • ??? ?????
  • Genome? ??
  • ??????
  • HGP ??? ????
  • ?????? ??

3
Genome
  • ??? ???
  • ???(gene), ???(genome)

4
Great 3 books
  • ?? ?? - ??

5
Central Dogma of Molecular Biology
6
(No Transcript)
7
Protein structure
  • 20 Amino acids
  • Sequence specifies conformation
  • RNase

8
Life
  • DNAs common method of producing more DNA
  • Review the life

9
Evolution
  • Self replicator

10
Chromosome
1 cM 1 Mbps
11
Gene structure
12
(No Transcript)
13
Junk DNA
  • ?? Genome? 5?? ???? ?? ??. ???? ?????
  • Repetitive sequence
  • LINE (gt300bps)
  • SINE (300bps), Alu (3000050000?)
  • Microsatelite

14
Human genome
  • 34x1014 cells (245)
  • gt 200 cell type
  • 3x109 bps (3Gbps 3Gbyte)
  • 2000025000 Genes
  • 98 unknown functional DNA
  • 0.1 difference with you
  • Information theory 30Mbyte

15
Human genome project
  • DOE, NHGRI ?? ??. 2003? ?? ??. 13?. 7?? ??
  • 95? ?? Junk DNA ? ? ? ?? ?? ??? ??? ????
  • ??
  • Human DNA ?? ?? Gene? ??
  • 30? ????? ??
  • Database? ??? ??
  • ?? ??? ? ?? ??? ??
  • ?? ??? ??? ??

16
History
  • PCR
  • RFLP
  • Genetic marker
  • BAC
  • Shotgun sequencing
  • Whole genome shotgun

17
Gel Electrophoresis
  • ?(???)? ??? ? ??? ??????, ???? ??. ???? ??
  • DNA, Protein

18
PCR
  • Polymerase Chain Reaction

19
Genetic marker
  • Polymorphic allele locus

20
(No Transcript)
21
Genetic map
22
Cloning
  • ?? ?? ? ??? ??? ?? ?? ? ??.
  • ???, ?? ? ?? ?? ?? ?? ??

23
Gene cloning
  • Gene cloning ??
  • Genome??? ??? ??? ???.
  • ??? ??? ??? ? ?? PrimerDesign? ??.
  • PCR? ????? major band? ????, ????.
  • CloningVector? ????.
  • Selection? ??? ??, ?? ???? ??? ??? ???? ??? ????.
  • Cloning vector
  • Plasmid
  • Cosmid 30 kb
  • BAC 350 kb
  • YAC 2 Mb ??
  • PAC 300 kb

24
DNA sequencing
25
DNA sequencing
26
DNA sequencing
  • Frederic Sanger
  • DNA, Protein
  • ????
  • 700-800bp

27
Shotgun sequencing
??? ?? ?? ?????? ?? ??? ?????? ?? ?, ????? ???? ?
???? ??? ??? ? ?? ??. ????? ?? ???? ?, ???
???????? ???? ???? ??? ??????. -- ?????, ?????
???
28
Genome sequencing
  • Clone by clone method
  • Genetic marker? ?? BAC ?? ? shotgun
  • Whole genome shotgun
  • ??? shotgun
  • Repeat ? ?? ???? ???.
  • ???? ???.

29
Current status (since 2003)
  • Human Chromosome 4 Completed, April 2005.
  • Human Chromosome 2 Completed, April 2005.
  • Human Chromosome X Completed, March 2005.
  • Human Chromosome 16 Completed, December 2004.
  • Human Gene Count Estimates Changed to 20,000 to
    25,000, October 2004.
  • Human Chromosome 5 Completed, September 2004.
  • Human Chromosome 9 Completed, May 2004.
  • Human Chromosome 10 Completed, May 2004.
  • Human Chromosome 19 Completed, March 2004.
  • Human Chromosome 13 Completed, March 2004.
  • Human Chromosome 6 Completed, October 2003.
  • Human Chromosome 7 Completed, July 2003.
  • Human Chromosome Y Completed, June 2003.
  • Human Genome Project Completion 1990-2003 (April
    2003)

30
Genome browser
  • UCSC Genome browser
  • NCBI Genome browser
  • Ensembl
  • VistaBrowser

31
Genetic disease before HGP
32
Genetic disease after HGP
33
Comparative genomics
  • Synteny (Gene order), Gene duplication, Gene
    fusion

34
(No Transcript)
35
Comparative genomics
36
SNP
  • Single Nucleotide Polymorphism
  • ?? ??? ? ?? ???
  • ???? ? ???? ? ?????? ? ????

37
Haplotype
38
(No Transcript)
39
HapMap
  • ??, ??, ??, ???, ??, ?????
  • Project? ??? MinorAllele? ??? ?? 5 ???? ?? ??? 5
    kilobase ? 60?? SNPs? genotype ?? ?

40
Transcriptome, Proteome
  • EST
  • DNA chip
  • Proteomics

41
EST
  • Expression Sequence Tag

42
(No Transcript)
43
(No Transcript)
44
(No Transcript)
45
Transformational grammar
  • Regular grammar computer program
  • Context free grammar DNA
  • Palindrome, ?? ?????
  • Context sensitive grammar
  • Unrestricted Grammar ???

46
Sequence alignment
47
Smith-Waterman algorithm
48
BLAST
  • Unknown sequence

Known sequence Database
49
Object oriented programming
  • Computer programming paradigm
  • ????? ???

50
???
  • Rosetta stone
  • Programming
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