1. 2010/05/06
kaneko.satoko(at)ocha.ac.jp

2. Mac OS X
(NCBI, Ensembl)

3. Mac OS X
OS/CUI GUI/ /
/ / /
pwd/mkdir/cd/ls/less/rm/rmdir

4. OS
OS(OperaIng System)
Windows Mac OS
*Mac OS X UNIX
CUI GUI
OS
UNIX Linux (
) CUI (Character User Interface)
Windows Mac
GUI (Graphical User Interface)
CUI
GUI

5.
Mac OS
$ ( )
(Perl, Ruby,
Java )
/
( echo $PATH )

7.
(UNIX )
Mac Users
bin
dev
etc
root
sbin
usr
home
var
tg01
tg02
tg03
bin
dev
etc
root
sbin
usr
home (Users)
var

8.
(PATH)
/
bin
Users
usr
var
/bin
/Users
/usr
/var
tg01
tg02
/Users/tg01
/Users/tg02
sample1.txt /Users/tg01/sample1.txt

9.
tg01
./..
..
./../..
bin
Users
usr
var
./../../bin
./..
./../../usr
./../../var
. tg01
tg02
.
./../tg02
sample1.txt ./sample1.txt
./

10.
[Enter]
‘‐’
$ man ls man(manual)
ls
$ ls –a /Users/tg02 /Users/tg02 “‐a” “.”

11. (1)
pwd (Print Work Directory)
tg01
$ pwd
[ /Users/tg01]
mkdir (MaKe DIRectory)
tg01
$ mkdir data
[Finder ]
data

12. (2)
cd (Change Directory)
tg01
$ cd
[ $cd /Users/tg01/data
$cd data]
data
cd
CotEditor
name.txt
data
data
a b
Finder

13. (3)
ls (LiSt directory) tg01
$ ls
[$ls data
data
a b name.txt]
name.txt
$ls –a
a
b
less
$ less
[$less name.txt
]
q

14. (4)
rm (ReMove file)
$ rm
[$rm name.txt]
$ls name.txt
rmdir (ReMove DIRectory)
$ rmdir
[$rm a]
$ rm –rf
‐rf
$ls ‐a data
UNIX

15. 1)
2) bin [/Users/tg01]
3)
4) bin
5)
bin
tab
aabbccdd bbccddee
ls aa[tab] ls aabbccdd aa
page , page
Web
hip://www.k‐tanaka.net/unix/
hip://www5.plala.or.jp/vaio0630/kp/command.htm

16.
NCBI
Ensembl
NCBI Ensembl

17. ( TV)

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

19. NCBI
NCBI

20. NCBI
hip://www.ncbi.nlm.nih.gov/
NCBI NaIonal Center for Biotechnology InformaIon
(NIH) NLM NaIonal Library of Medicine
1 1988
NCBI (2010 4 )

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

22. NCBI Viewer keyword
1991 Buck and Axel
1082 1082
query [olfactory receptor] 31395 hit
["olfactory receptor gene" AND rat AND Olr1082]
""
AND
GenBank

23. NCBI Viewer
[Macintosh HD/ /tg02/
] sequence.fasta

24. NCBI Viewer
i) Accession number
Search NucleoIde for Accession number
ii) [Links] [PubMed]
iii) [All links from this record]
[NucleoIde]
[Cited in PMC]

25. 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:

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

27. Ensembl
Ensembl
Ensembl viewer keyword
(4): Synteny
(5): Ortholog, Paralog, Homolog
(6):
(7):
(8): Gene Ontology

28. Ensembl
Ensembl

29. Ensembl
hip://www.ensembl.org/
Ensembl EMBL‐EBI( ) Sangar InsItute( )
2000
NCBI ( )

30. Ensembl Viewer keyword
NCBI
1082 1082
query [olfactory receptor] Ensembl
olfactory receptor
Search for [rat Olr1082]
e.g. human gene BRCA2or rat X:100000..200000 or insulin
query [ ], [ ], [ ]

31. Ensembl Viewer
Browse a Genome

32.
query

33. (1)
LocaIon

34. (2)
ComparaIve Genomics( )
GeneIc VariaIon( )
Markers(
sequence tagged site (STS) )
Configure this page
Export data

35. ‐Region in detail‐
Ensembl
annotate

36. ‐Configure this page1‐
Configure this page
Save and close
Ensembl

37. ‐Configure this page2‐
conIg start/stop codon
Affymetrix microarray
probe
repeat

38. ‐Configure this page3‐
genome
alignment
BLASTZ
GC

39. ‐Configure this page4‐
Synteny

40. ‐Synteny‐
7
synteny
13 (chicken,
chimpanzee, cow, dog,
horse, macaque, mouse,
opossum, orangutan )
3 (dog, human, rat)
synteny

41. (4) Synteny ( )
rearrangement
1 1
22 19

42. (1)
Gene ID ID

43. (2)

44. ‐Gene summary‐
Ensembl ID
ConIg

45. ‐Splice variants‐
alternaIve splicing
splicing variant

46. ‐SupporIng evidence‐
Ensembl
Ensembl
NCBI NCBI
alignment
Olr1082
Olr1081

47. ‐Marked‐up sequence‐
exon
Exon
Configure this page

48. ‐RegulaIon‐
rat Olr1082
( sonic hedgehog)
cisRED (cis‐regulatory element database):
CTCF (CCCTC‐binding factor): zinc‐finger protein (insulaIon)

49. ‐Genomic alignments‐
alignment
Select an alignment

50. –Gene Tree‐
alignment
maximum likelihood

51. –Gene Tree (text)‐
0.006
0.029
0.006
0.165
0.035
((((human :0.006, chimpanzee :0.006) :0.029, 0.180
macaque :0.035) :0.165),
(mouse :0.02, rat :0.02) :0.180);
0.020
0.020

52. –Gene Tree (alignment) 1‐
Gene Tree alignment
MSF format:
ID
ID
Configure this page alignment

53. –Gene Tree (alignment) 2‐
FASTA
>
alignment
NEXUS
#NEXUS ntax( ),
nchar( )
alignment 10

54. –Orthologues‐
ortholog
Species:
Type: Ortholog
( )
dN/dS: /
( )
Ensembl idenHfier: Ensembl ID
External ref.: Ensembl
ID

55. (5): Ortholog, Paralog, Homolog
a
a
a'
a1
a'1
a2
a'2
1
2
a a' 1 2
(ortholog): (a1 a2 a'1 a'2)
(paralog): (a1 a'1 a2 a'2 a1 a'2 a'1 a2)
(homolog):

56. (5): Ortholog, Paralog – ‐
a
t1
a
a'
t2
a1
a'1
a2
a'2
1
2
( , molecular clock)
ortholog 2 t2 ( a1 a2 )
paralog a1 a'1 a
2 (t1+t2) ( a1 a'1 )
ortholog paralog
(ortholog paralog )
( )

57. (6):
Coding Sequence 2
(synonymous subsItuIon)
(nonsynonymous subsItuIon)
dS, Ks (the rate of synonymous subsItuIons)
dN, Ka (the rate of nonsynonymous subsItuIons)
2nd base
1st base
3rd base
AUG
U
C
A
G
UUU
Phe
UCU
Ser
UAU
Tyr
UGU
Cys
U
UAA, UAG, UGA
UUC
Phe
UCC
Ser
UAC
Tyr
UGC
Cys
C
U
UUA
Leu
UCA
Ser
UAA
stop
UGA
stop
A
1st
UUG
Leu
UCG
Ser
UAG
stop
UGG
Trp
G
CUU
Leu
CCU
Pro
CAU
His
CGU
Arg
U
(Leu, Arg)
CUC
Leu
CCC
Pro CAC
His
CGC
Arg
C
C
CUA
Leu
CCA
Pro
CAA
Gln
CGA
Arg
A
CUG
Leu
CCG
Pro CAG
Gln
CGG
Arg
G
2nd
AUU
Ile
ACU
Thr
AAU
Asn
AGU
Ser
U
AUC
Ile
ACC
Thr
AAC
Asn
AGC
Ser
C
A
AUA
Ile
ACA
Thr
AAA
Lys
AGA
Arg
A
AUG
Met
ACG
Thr
AAG
Lys
AGG
Arg
G
GUU
Val
GCU
Ala
GAU
Asp
GGU
Gly
U
GUC
Val
GCC
Ala
GAC
Asp
GGC
Gly
C
G
GUA
Val
GCA
Ala
GAA
Glu
GGA
Gly
A
GUG
Val
GCG
Ala
GAG
Glu
GGG
Gly
G

58. –Orthologues ‐
ortholog_one2one: 1 1
ortholog_one2many:
ortholog_many2many:
apparent_ortholog_one2one: 3

59. –Paralogues‐
paralog

60. –Protein families‐
Family ID: ID
Olr1082 57
Consensus annotaHon:
Other Rat transcripts in this family:
MulHple alignments: alignment

61. –VariaIon Table (1)‐
Ambiguity
Code
Represents
Y
Pyrimidine (C&T)
R
Purine (A&G)
ID: SNP ID ( SNP 100bp ) W
weak (A&T)
Type: SNP ( / UTR ) S
strong (G&C)
Chr: bp: (bp) K
keto (T&G)
Alleles: M
amino (C&A)
Ambiguity: variaIon D
not C
AA change: V
not T
AA co‐ordinate: ( ) H
not G
Class: inserIon B
not A
Source: variaIon X/N
unknown
ValidaHon: variaIon (frequency hapmap )

62. (7):
(polymorphism) (subsItuIon)
1 (mutaIon)
(advantageous) (neutral) (deleterious)

63. (7): –alignment ‐
( )
( )
10 20
T······A·· ······C··G
·······A·· ·C····C··G
T······A·· ······C··G
T······A·· ·C····C···
····C··A·· ······C···
CAGGGCATCC GTCCTCGCCA
·TC······· ····C···G·
·T·······T ····C·····
·T·······T ····C··C··
·T····T··T ····C·····
·T········ ····C···G·

64. –VariaIon Table (2)‐
VariaIon Table Configure this page
VariaHon source: variaIon
VariaHon class: variaIon
Heterozygous variaIon: 1 variaIon
MNPs: MulI NucleoIde Polymorphisms
ValidaHon: variaIon
VariaHon type: variaIon
DAS source: (DAS Distributed AnnotaIon System )
Display opHons:

65. –ID History‐
ID version
Assembly( ) version
gap

66. Transcript summary
Ensembl ID ( ) (Ra#us norvegicus )
ENSG… Gene ENSRNOG… Rat Gene
ENST… Transcript ENSRNOT… Rat Transcript
ENSE… Exon ENSRNOE… Rat Exon
ENSP… Protein
ENSRNOP… Rat Protein

67. –SupporIng evidence, Exons‐
NCBI
exon, intron, 5' upstream,
3' downstream

68. –cDNA sequence‐
splicing exon
variaIon
variaIon

69. –Protein sequence‐
( )
indel
splice

70. –General idenIfiers‐
ID
alignment

71. –Oligo probes‐
microarray oligo probe
[view all locaIons]
oligo probe
oligo probe 25bp

72. –Gene ontology‐
Gene ontology
Evidence
IC ‐ Inferred by Curator
IDA‐ Inferred from Direct Assay
IEA ‐ Inferred from Electronic AnnotaIon
IEP ‐ Inferred from Expression Paiern
IGI ‐ Inferred from GeneIc InteracIon
IMP ‐ Inferred from Mutant Phenotype
IPI ‐ Inferred from Physical InteracIon
ISS ‐ Inferred from Sequence or Structural Similarity
NAS ‐ Non‐traceable Author Statement
ND ‐ No biological Data available
RCA ‐ inferred from Reviewed ComputaIonal
Analysis
TAS ‐ Traceable Author Statement
Gene Ontology NR ‐ Not Recorded

73. (8): Gene Ontology
Gene Ontology (GO)
GO GO Term Go Term 3
biological process
cellular component
molecular funcIon
olfactory receptor gene
molecular_funcIon [GO:0003674]
molecular transducer acIvity [GO:0060089]
signal transducer acIvity [GO:0004871]
receptor acIvity [GO:0004872]
transmembrane receptor acIvity [GO:0004888]
G‐protein coupled receptor acIvity [GO0004930]
rhodopsin‐like receptor acIvity [GO:0001584]

74. –PopulaIon comparison,
Comparison image‐
Comarison Image
PopulaIon comparison

75. –Protein summary‐

76. –Domains & features‐
[Display all genes with domain]

77. –Transcript ID History‐
ID
version
version
annotaIon

78. Ensembl 104 (2010 4 )
version
NCBI 108 (2010 4 )

79.
(NCBI Ensembl) viewer
‐ version Ensembl