SlideShare a Scribd company logo

080806

•
•
S
sesejun

1) The document describes various bioinformatics databases and tools for analyzing genomic and biological sequence data, including NCBI, Ensembl, FASTA format, and the UNIX file system. 2) It provides examples of common UNIX commands like pwd, mkdir, cd, ls, and less. 3) It compares command-line interfaces (CUI) used in UNIX systems with graphical user interfaces (GUI) used in operating systems like Windows and Mac.

Related slideshows

100422-intro,setup
100422-intro,setup100422-intro,setup
100422-intro,setup
 
The VR Continuum: From CAVEs to Digital TV, How VR and AR will change everyda...
The VR Continuum: From CAVEs to Digital TV, How VR and AR will change everyda...The VR Continuum: From CAVEs to Digital TV, How VR and AR will change everyda...
The VR Continuum: From CAVEs to Digital TV, How VR and AR will change everyda...
 
มโนท ศน เทคโนโลย_ทางการศ_กษา
มโนท ศน เทคโนโลย_ทางการศ_กษามโนท ศน เทคโนโลย_ทางการศ_กษา
มโนท ศน เทคโนโลย_ทางการศ_กษา
 
1 of 56
20 DB 2008/08/06 kaneko.satoko(at)ocha.ac.jp
20 DB
PC UNIX NCBI Ensembl NCBI Ensembl viewer
(1):
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)
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
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
(a) (b) (c) Figure
Figure Figure
(1) ATGC 35 1946 (DNA ) 8/20=40% 16/19=84%
PC OS Emacs or CotEditor [ CotEditor ] MacPorts (Norton AntiVirus) ( )
Dock
Finder
080806
UNIX OS/CUI GUI/ / / / / pwd/mkdir/cd/ls/less/rm/rmdir
OS OS Windows Mac OS (Operating System) OS CUI GUI OS UNIX Linux ( ) CUI (Character User Interface) OS Windows Mac GUI (Graphical User Interface)
Mac OS (UNIX ) (Perl, Ruby, Java ) / ( )
Macintosh HD/ /     Dock       Dock
                 
Mac Users bin dev etc root sbin usr home var tg01 tg02 tg03 bin dev etc root sbin usr home (Users) var
(PATH) / bin Users usr var /bin /Users /usr /var tg01 tg02 /Users/tg01 /Users/tg02 sample1.txt /Users/tg01/sample1.txt
tg01 ./.. .. ./../.. bin Users usr var ./../../bin ./.. ./../../usr ./../../var . tg01 tg02 . ./../tg02 sample1.txt ./sample1.txt ./
(1) pwd (Print Work Directory) tg02 $ pwd [ /Users/tg02] data mkdir (MaKe DIRectory) tg02 $ mkdir data [Finder ] data
(2) cd (Change Directory) tg02 $ cd [ $cd /Users/tg02/data $cd data] data
(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
(4) rmdir (ReMove DIRectory) $ rmdir UNIX
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
DNA - (2):
1958 Francis Crick (DNA) DNA RNA RNA replication transcription translation ( ) ( ) ( ) reverse transcription ( ) splicing ( ) RNA (non-coding RNA)
(genome)  DNA /PCR              SNPs         (SNPs)  DNA /     SSCP/Heteroduplex     cDNA   (transcriptome)                    2D‐PAGE   (proteome)  in vitro translaAon             /2D‐PAGE         TOF‐MS/NMR/Two‐hybrid   
(2): 5' 3'
DNA   GenBank( ) EMBL( ) DDBJ( ) UCSC( )  (SNPs)  dbSNP( ) JSNP( ) �� OMIM( ) MutaAon database( ) SWISS‐PROT( ) PIR( ) Pfam( ) PROSITE( ) BLOCKS( ) PDB( ) SCOP( ) CATH( ) KEGG( ) MEDLINE( ) NCBI( ) Ensembl( )
NCBI NCBI NCBI viewer query /keyword / / DDBJ/EMBL/GenBank (3): FASTA
NCBI http://www.ncbi.nlm.nih.gov/ NCBI National Center for Biotechnology Information (NIH) NLM National Library of Medicine 1 1988
NCBI Viewer query NCBI Search [All Databases] for [query] olfactory receptor NCBI query
NCBI Viewer keyword GenBank
NCBI Viewer [Display] [FASTA] DNA fasta [Send to] [Text] [FASTA], [Text] [File]
NCBI Viewer i) Accession number Search Nucleotide for Accession number ii) [Links] [Nucleotide] [Related Articles]
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:       
(3): FASTA FASTA 1 1 '>' 2 2 (query) ( )
Ensembl Ensembl Ensembl viewer keyword Ensembl Gene Report 1,2 (4):
Ensembl http://www.ensembl.org/index.html Ensembl EMBL-EBI( ) Sangar Institute( ) 2000 NCBI ( )
Ensembl Viewer keyword
080806
Ensembl Gene Report 1
Ensembl Gene Report Oligo Matches: microarray hit GO: Gene Ontology InterPro: InterPro Protein Family: Ensembl Trasncript structure: Protein features:
(4): 1 2 a b 1 2 (ortholog): (a1 a2 b1 b2) (paralog): (a1 b1 a2 b2 a1 b2 b1 a2)
Gene Report Export gene data
080806
ContigView
Detailed View Ensembl Gene ID
Ensembl Viewer
Ensembl Viewer 1 BLAT GC 40% 45%
Ensembl Viewer 2 GC% GC% A T PCR GC primer G C Figure 4‐4  Molecular Biology of the Cell (© Garland Science 2008) 
080806
(NCBI Ensembl) viewer

More Related Content

080806

  • 1. 20 DB 2008/08/06 kaneko.satoko(at)ocha.ac.jp
  • 2. 20 DB
  • 3. PC UNIX NCBI Ensembl NCBI Ensembl viewer
  • 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
  • 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
  • 19.                  
  • 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
  • 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
  • 51. Detailed View Ensembl Gene ID
  • 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