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080806

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  • 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
  • 14. UNIX OS/CUI GUI/ / / / / pwd/mkdir/cd/ls/less/rm/rmdir
  • 15. OS OS Windows Mac OS (Operating System) OS CUI GUI OS UNIX Linux ( ) CUI (Character User Interface) OS Windows Mac GUI (Graphical User Interface)
  • 16. Mac OS (UNIX ) (Perl, Ruby, Java ) / ( )
  • 17. Macintosh HD/ /     Dock       Dock
  • 18.                  
  • 19. Mac Users bin dev etc root sbin usr home var tg01 tg02 tg03 bin dev etc root sbin usr home (Users) var
  • 20. (PATH) / bin Users usr var /bin /Users /usr /var tg01 tg02 /Users/tg01 /Users/tg02 sample1.txt /Users/tg01/sample1.txt
  • 21. tg01 ./.. .. ./../.. bin Users usr var ./../../bin ./.. ./../../usr ./../../var . tg01 tg02 . ./../tg02 sample1.txt ./sample1.txt ./
  • 22. (1) pwd (Print Work Directory) tg02 $ pwd [ /Users/tg02] data mkdir (MaKe DIRectory) tg02 $ mkdir data [Finder ] data
  • 23. (2) cd (Change Directory) tg02 $ cd [ $cd /Users/tg02/data $cd data] data
  • 24. (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
  • 25. (4) rmdir (ReMove DIRectory) $ rmdir UNIX
  • 26. 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
  • 27. DNA - (2):
  • 28. 1958 Francis Crick (DNA) DNA RNA RNA replication transcription translation ( ) ( ) ( ) reverse transcription ( ) splicing ( ) RNA (non-coding RNA)
  • 29. (genome)  DNA /PCR              SNPs         (SNPs)  DNA /     SSCP/Heteroduplex     cDNA   (transcriptome)                    2D‐PAGE   (proteome)  in vitro translaAon             /2D‐PAGE         TOF‐MS/NMR/Two‐hybrid   
  • 30. (2): 5' 3'
  • 31. DNA   GenBank( ) EMBL( ) DDBJ( ) UCSC( )  (SNPs)  dbSNP( ) JSNP( )   OMIM( ) MutaAon database( ) SWISS‐PROT( ) PIR( ) Pfam( ) PROSITE( ) BLOCKS( ) PDB( ) SCOP( ) CATH( ) KEGG( ) MEDLINE( ) NCBI( ) Ensembl( )
  • 32. NCBI NCBI NCBI viewer query /keyword / / DDBJ/EMBL/GenBank (3): FASTA
  • 33. NCBI http://www.ncbi.nlm.nih.gov/ NCBI National Center for Biotechnology Information (NIH) NLM National Library of Medicine 1 1988
  • 34. NCBI Viewer query NCBI Search [All Databases] for [query] olfactory receptor NCBI query
  • 35. NCBI Viewer keyword GenBank
  • 36. NCBI Viewer [Display] [FASTA] DNA fasta [Send to] [Text] [FASTA], [Text] [File]
  • 37. NCBI Viewer i) Accession number Search Nucleotide for Accession number ii) [Links] [Nucleotide] [Related Articles]
  • 38. 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:       
  • 39. (3): FASTA FASTA 1 1 '>' 2 2 (query) ( )
  • 40. Ensembl Ensembl Ensembl viewer keyword Ensembl Gene Report 1,2 (4):
  • 41. Ensembl http://www.ensembl.org/index.html Ensembl EMBL-EBI( ) Sangar Institute( ) 2000 NCBI ( )
  • 42. Ensembl Viewer keyword
  • 43. Ensembl Gene Report 1
  • 44. Ensembl Gene Report Oligo Matches: microarray hit GO: Gene Ontology InterPro: InterPro Protein Family: Ensembl Trasncript structure: Protein features:
  • 45. (4): 1 2 a b 1 2 (ortholog): (a1 a2 b1 b2) (paralog): (a1 b1 a2 b2 a1 b2 b1 a2)
  • 46. Gene Report Export gene data
  • 47. ContigView
  • 48. Detailed View Ensembl Gene ID
  • 49. Ensembl Viewer
  • 50. Ensembl Viewer 1 BLAT GC 40% 45%
  • 51. Ensembl Viewer 2 GC% GC% A T PCR GC primer G C Figure 4‐4  Molecular Biology of the Cell (© Garland Science 2008) 
  • 52. (NCBI Ensembl) viewer