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???? (Bioinformatics)

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(Bioinformatics) E-mail: d7526010_at_csie.ntu.edu.tw Please tell me Why you are here? Make a definition of bioinformatics Introduction What is ... – PowerPoint PPT presentation

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Title: ???? (Bioinformatics)


1
????(Bioinformatics)
  • ???
  • E-mail d7526010_at_csie.ntu.edu.tw

2
Please tell me
  • Why you are here?
  • Make a definition of bioinformatics

3
Introduction
  • What is bioinformatics?
  • Why bioinformatics?
  • The past, current, and future in bioinformatics

4
?????????
  • ??????????
  • ?????????????????????
  • ???????????????
  • ??????
  • ???????????????
  • ??????, ??, ???????????
  • ????????????????

5
???????????
6
REVOLUTION IN BIO-MEDICAL RESEARCH
Differential Display Subtraction
Library Real-Time PCR Microarray 2-Dimensional
Protein Electrophoresis Serial Analysis of Gene
Expression Expression Sequence Tags
Northern Hybridization Western Hybridization South
ern Hybridization RFPD
7
???????????
  • ???????????,??????,????????

8
The GeneBank Data (9/25/2002)
Year Base Pairs Sequences
1982 680338 606
1983 2274029 2427
1984 3368765 4175
1985 5204420 5700
1986 9615371 9978
1987 15514776 14584
1988 23800000 20579
1989 34762585 28791
1990 49179285 39533
1991 71947426 55627
1992 101008486 78608
1993 157152442 143492
1994 217102462 215273
1995 384939485 555694
1996 651972984 1021211
1997 1160300687 1765847
1998 2008761784 2837897
1999 3841163011 4864570
2000 11101066288 10106023
2001 15849921438 14976310
9
Protein DataBank Data (9/25/2002)
10
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  • ???????????,??????,????????
  • ????????????,??????????,??????????
  • ???????????????????
  • ???????????????????

11
?????????
12
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???(genome)
  • All the genetic material in the chromosomes of a
    particular organism
  • Its size is generally given as its total number
    of base pairs.

14
??????
  • Human 3000 million bases
  • Mouse 3000 million bases
  • Drosophila (fruit fly) 165 million bases
  • Nematode (roundworm) 100 million bases
  • Yeast (fungus) 14 million bases
  • E. coli (bacteria) 4.67 million bases

15
?????????
  • ???HGP (Human Genome Project)
  • ?????
  • identify all the genes in human DNA,
  • determine the sequences of the 3 billion chemical
    bases that make up human DNA
  • store this information in databases
  • develop tools for data analysis
  • transfer related technologies to the private
    sector
  • address the ethical, legal, and social issues
    (ELSI) that may arise from the project

16
Human Genome
17
HGP??????
  • HGP?1990??????
  • HGP??????????????????
  • 2000????Celera???????????????????

18
HGP??????(?)
  • 2001?2?
  • Initial sequencing and analysis of the human
    genome (Nature, Vol. 409, 15 Feb. 2001, by
    International Human Genome Sequencing Consortium)
  • The sequence of the human genome (Science, Vol.
    291, 16 Feb. 2001, by J. C. Venter, et al.)

19
Biology moves into the silicon stage

in vivo
in vitro
in silico
20
?HGP????????????
21
Before HGP
  • String analysis
  • Pair-wise, multiple sequence alignment

22
Sequence Analysis? Alignment
  • Pair-wise alignment
  • SURVIVE SURVIVE
  • SURIUE SUR- IUE
  • Multiple sequence alignment

RPCVCPVLRQAAQ s1 RPCVC_
P__VLRQAAQ a1 RPCACCPVLRQVVQ s2
RPCACCP__VLRQVVQ a2 KPCLCPRQLRQV
s3 KPCLC_ P RQLRQV_ _ a3 KPCCPRQAAQ
s4 KPC_C_ P____ RQAAQ a4 S A
23
Before HGP
  • String alignment
  • Pair-wise, multiple alignment
  • Linkage analysis

24
Linkage Analysis
25
Before HGP
  • String alignment
  • Pair-wise, multiple alignment
  • Linkage analysis
  • Phylogenetic tree

26
Phylogenetic Tree
27
Phylogenetic Tree
28
Before HGP
  • String alignment
  • Pair-wise, multiple alignment
  • Linkage analysis
  • Phylogenetic tree
  • Protein structure prediction

29
Protein Structure Prediction
30
During HGP
  • Sequencing
  • Physical mapping
  • Fragment assembly

31
Sequencing Strategies (1)
  • Map-Based Assembly
  • Create a detailed complete fragment map
  • Time-consuming and expensive
  • Provides scaffold for assembly
  • Original strategy of Human Genome Project

32
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Sequencing Strategies (2)
  • Shotgun
  • Quick, highly redundant requires 7-9X coverage
    for sequencing reads of 500-750bp. This means
    that for the Human Genome of 3 billion bp, 21-27
    billion bases need to be sequence to provide
    adequate fragment overlap.
  • Computationally intensive
  • Troubles with repetitive DNA
  • Original strategy of Celera Genomics

34
Shotgun Sequencing Assembly of Random Sequence
Fragments
  • To sequence a Bacterial Artificial Chromosome
    (100-300Kb), millions of copies are sheared
    randomly, inserted into plasmids, and then
    sequenced. If enough fragments are sequenced, it
    will be possible to reconstruct the BAC based on
    overlapping fragments.

35
During HGP
  • Sequencing
  • Physical mapping
  • Fragment assembly
  • Gene Prediction

36
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38
During HGP
  • Sequencing
  • Physical mapping
  • Fragment assembly
  • Gene Prediction

39
After HGP (Post Genomic)
  • Microarray

40
Microarray
41
After HGP (Post Genomic)
  • Microarray
  • Regulatory network

42
Regulatory Network ? Simplified representation of
the NF- B network.
43
After HGP (Post Genomic)
  • Microarray
  • Regulatory network
  • Proteomics

44
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??????????
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50
????????(1)
  • ??(sequencing)
  • ????DNA????,???????????,????????????????????
  • ?????????????????????,??????????????????????

51
????????(2)
  • ????(sequence analysis)
  • ?????????,????????
  • ??????(genomics)?????
  • DNA??????
  • ?????????
  • ??????
  • ???????
  • ??????
  • SNP (Single nucleotide polymorphism)
  • Haplotypes

52
????????(3)
  • ????(gene finding)
  • ?????????,?????????
  • ??????????DNA??,??????????????????????????????????
    ???
  • ??????,??????????????????????

53
????????(4)
  • ???????(bioinformatics database)
  • ?????????????,???????????????????
  • ?????????????,??????,?????????????????????????????
    ???????????????,?????????????????????

54
????????(5)
  • ????????(protein structure prediction)
  • ??????????????????
  • X-ray?NMR???????????????
  • ???????????????????,??????????????

55
????????(6)
  • ????(proteomics)
  • methodological developments in protein separation
    and characterization
  • advances in bioinformatics, and
  • novel applications of proteomics in all areas of
    the life sciences and industry.
  • (These endeavours give new insights into protein
    functions, interactions and pathways.)

56
????????(7)
  • ??????(evolutionary tree construction)
  • ??????????????????
  • ????????(character)????????????
  • ??????????????????
  • ?????????????NP-Complete (????,?????????)

57
????????(8)
  • ????
  • RNA??????(RNA secondary structures)
  • ??????(comparative genomics)
  • ????(genetic networks)
  • ?????(microarrays ??????)
  • ?????(molecular computers)

58
?????????
59
Bioinformatics and Computational Biology-Related
Journals
  • Bioinformatics (?????CABIOS)
  • Bulletin of Mathematical Biology
  • Computers and Biomedical Research
  • Genome Research
  • Genomics
  • Journal of Computational Biology
  • Journal of Molecular Biology
  • Nature
  • Science

60
Bioinformatics and Computational Biology-Related
Conferences
  • the first IEEE Computer Society Bioinformatics
    Conference (CSB 2002, CA, USA)
  • Intelligent Systems for Molecular Biology (ISMB
    2003, Brisbane, Australia)
  • Pacific Symposium on Biocomputing(PSB 2003,
    Kauai, Hawaii, USA)
  • The Seventh Annual International Conference on
    Research in Computational Molecular
    Biology (RECOMB 2003, Berlin, Germany)

61
Bioinformatics and Computational Biology-Related
Books
  • Calculating the Secrets of Life Applications of
    the Mathematical Sciences in Molecular Biology,
    by Eric S. Lander and Michael S. Waterman (1995)
  • Introduction to Computational Biology Maps,
    Sequences, and Genomes, by Michael S. Waterman
    (1995)
  • Introduction to Computational Molecular Biology,
    by Joao Carlos Setubal and Joao Meidanis (1996)
  • Algorithms on Strings, Trees, and Sequences
    Computer Science and Computational Biology, by
    Dan Gusfield (1997)
  • Computational Molecular Biology An Algorithmic
    Approach, by Pavel Pevzner (2000)
  • Introduction to Bioinformatics, by Arthur M. Lesk
    (2002)

62
?????????
  • MIT Biology Hypertextbook
  • http//www.mit.edu8001/afs/athena/course/other/es
    gbio/www/7001main.html
  • ????on-line???
  • The International Society for Computational
    Biology
  • http//www.iscb.org/
  • National Center for Biotechnology Information
    (NCBI, NIH)
  • http//www.ncbi.nlm.nih.gov/
  • (NCBI, EBI ? DDBJ??????????????,????????)
  • European Bioinformatics Institute (EBI)
  • http//www.ebi.ac.uk/
  • DNA Data Bank of Japan (DDBJ)
  • http//www.ddbj.nig.ac.jp/

63
????????????
  • ??????,????????????????
  • ????????????????,?????????????????
  • ????????????,??????????,????????

64
?????
  • ??????
  • Credits
  • ?????
  • ??????
  • ???????????????????????????????
  • Theory Practice

??????
?????
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