1. 20
DB
2008/08/06
kaneko.satoko(at)ocha.ac.jp

2. 20 DB

3. PC
UNIX
NCBI Ensembl
NCBI Ensembl viewer

4. (1):

5. 1953 DNA
1966 ( )
1972 Figure
1975-7
1985 PCR
1986
(Watson & Crick
Nature 1953 737,738)
1993
1995 DNA
1997 E.coli ( ) (4.6Mb)
2000
2003 (3.3Gb)

6. 1972
1975-7 (Sanger Maxam-Gilbert )
1985 PCR (6kb = 6000bp/day)
1986 DNA
1993
2000 (600kb = 600,000bp/day)
2007 Microarray like sequence (600Mb = 600,000,000bp/day)
2010 (100Gb = 100,000,000,000bp/hour)
(3.3Gb) 4

7. 1971 MEDLINE
1980 DNA
EMBL(European Molecular Biology Laboratory)
1982 DNA GenBank
1985 FASTA
1986 Swiss-Prot
1988 NCBI(National Center for Biotechnology Information)
Human Genome Initiative Bioinformatics
CLUSTAL
1990 BLAST
1991 World Wide Web
2000 Ensembl , 2001 UCSC

8. (a)
(b)
(c)
Figure

9. Figure
Figure

10. (1)
ATGC
35
1946 (DNA )
8/20=40%
16/19=84%

11. PC
OS
Emacs or CotEditor [ CotEditor ]
MacPorts
(Norton AntiVirus)
( )

12. Dock

13. Finder

15. UNIX
OS/CUI GUI/ /
/ / /
pwd/mkdir/cd/ls/less/rm/rmdir

16. OS
OS
Windows Mac OS (Operating System)
OS
CUI GUI
OS
UNIX Linux (
) CUI (Character User Interface) OS
Windows Mac
GUI (Graphical User Interface)

17. Mac OS
(UNIX )
(Perl, Ruby,
Java )
/
( )

18. Macintosh HD/ /
Dock
Dock

20. Mac Users
bin
dev
etc
root
sbin
usr
home
var
tg01
tg02
tg03
bin
dev
etc
root
sbin
usr
home (Users)
var

21. (PATH)
/
bin
Users
usr
var
/bin
/Users
/usr
/var
tg01
tg02
/Users/tg01
/Users/tg02
sample1.txt /Users/tg01/sample1.txt

22. tg01
./..
..
./../..
bin
Users
usr
var
./../../bin
./..
./../../usr
./../../var
. tg01
tg02
.
./../tg02
sample1.txt ./sample1.txt
./

23. (1)
pwd (Print Work Directory)
tg02
$ pwd
[ /Users/tg02]
data
mkdir (MaKe DIRectory)
tg02
$ mkdir data
[Finder ]
data

24. (2)
cd (Change Directory)
tg02
$ cd
[ $cd /Users/tg02/data
$cd data]
data

25. (3)
ls (LiSt directory)
tg02
$ ls
[$ls data
a b name.txt] data
$ls –a
name.txt
less a
b
$ less
[$less name.txt
]
q

26. (4)
rmdir (ReMove DIRectory)
$ rmdir
UNIX

27. 1)
2) bin
3)
4) bin
5)
6) blat
tab
aabbccdd bbccddee
ls aa[tab] ls aabbccdd aa
Web
http://www.k-tanaka.net/unix/
http://www5.plala.or.jp/vaio0630/ftp/command.htm

28. DNA
- (2):

29. 1958 Francis Crick
(DNA)
DNA RNA
RNA
replication transcription translation
( )
( )
( )
reverse transcription
( )
splicing
( )
RNA (non-coding RNA)

30. (genome) DNA /PCR
SNPs
(SNPs) DNA /
SSCP/Heteroduplex
cDNA
(transcriptome)
2D‐PAGE
(proteome) in vitro translaAon
/2D‐PAGE
TOF‐MS/NMR/Two‐hybrid

31. (2):
5'
3'

32. DNA GenBank( ) EMBL( ) DDBJ( ) UCSC( )
(SNPs) dbSNP( ) JSNP( )
OMIM( ) MutaAon database( )
SWISS‐PROT( ) PIR( )
Pfam( )
PROSITE( ) BLOCKS( )
PDB( ) SCOP( ) CATH( )
KEGG( )
MEDLINE( )
NCBI( ) Ensembl( )

33. NCBI
NCBI
NCBI viewer
query /keyword / /
DDBJ/EMBL/GenBank
(3): FASTA

34. NCBI
http://www.ncbi.nlm.nih.gov/
NCBI National Center for Biotechnology Information
(NIH) NLM National Library of Medicine
1 1988

35. NCBI Viewer query
NCBI
Search [All Databases]
for [query]
olfactory receptor
NCBI
query

36. NCBI Viewer keyword
GenBank

37. NCBI Viewer
[Display]
[FASTA]
DNA fasta
[Send to] [Text]
[FASTA], [Text] [File]

38. NCBI Viewer
i) Accession number
Search Nucleotide for Accession number
ii) [Links]
[Nucleotide]
[Related Articles]

39. DDBJ/EMBL/GenBank
3
LOCUS:
DEFINITION:
ACCESSION:
DDBJ/EMBL/GenBank
VERSION:
KEYWORD:
SOURCE:
ORGANISM:
REFERENCE:
AUTHOR:
TITLE:
JOURNAL:
MEDLINE: MEDLINE
FEATURES:
CDS: Protein-coding sequence
ORIGIN:

40. (3): FASTA
FASTA
1 1
'>'
2
2
(query) ( )

41. Ensembl
Ensembl
Ensembl viewer keyword
Ensembl Gene Report 1,2
(4):

42. Ensembl
http://www.ensembl.org/index.html
Ensembl EMBL-EBI( ) Sangar Institute( )
2000
NCBI ( )

43. Ensembl Viewer keyword

45. Ensembl Gene Report 1

46. Ensembl Gene Report
Oligo Matches: microarray hit
GO: Gene Ontology
InterPro: InterPro
Protein Family: Ensembl
Trasncript structure:
Protein features:

47. (4):
1
2
a b 1 2
(ortholog): (a1 a2 b1 b2)
(paralog): (a1 b1 a2 b2 a1 b2 b1 a2)

48. Gene Report Export gene data

50. ContigView

51. Detailed View
Ensembl Gene ID

52. Ensembl Viewer

53. Ensembl Viewer 1
BLAT
GC
40% 45%

54. Ensembl Viewer 2
GC%
GC%
A
T
PCR
GC
primer
G
C
Figure 4‐4 Molecular Biology of the Cell (© Garland Science 2008)

56. (NCBI Ensembl) viewer