080806

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080806

  1. 1. 20 DB 2008/08/06 kaneko.satoko(at)ocha.ac.jp
  2. 2. 20 DB
  3. 3. PC UNIX NCBI Ensembl NCBI Ensembl viewer
  4. 4. (1):
  5. 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. 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. 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. 8. (a) (b) (c) Figure
  9. 9. Figure Figure
  10. 10. (1) ATGC 35 1946 (DNA ) 8/20=40% 16/19=84%
  11. 11. PC OS Emacs or CotEditor [ CotEditor ] MacPorts (Norton AntiVirus) ( )
  12. 12. Dock
  13. 13. Finder
  14. 14. UNIX OS/CUI GUI/ / / / / pwd/mkdir/cd/ls/less/rm/rmdir
  15. 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. 16. Mac OS (UNIX ) (Perl, Ruby, Java ) / ( )
  17. 17. Macintosh HD/ /     Dock       Dock
  18. 18.                  
  19. 19. Mac Users bin dev etc root sbin usr home var tg01 tg02 tg03 bin dev etc root sbin usr home (Users) var
  20. 20. (PATH) / bin Users usr var /bin /Users /usr /var tg01 tg02 /Users/tg01 /Users/tg02 sample1.txt /Users/tg01/sample1.txt
  21. 21. tg01 ./.. .. ./../.. bin Users usr var ./../../bin ./.. ./../../usr ./../../var . tg01 tg02 . ./../tg02 sample1.txt ./sample1.txt ./
  22. 22. (1) pwd (Print Work Directory) tg02 $ pwd [ /Users/tg02] data mkdir (MaKe DIRectory) tg02 $ mkdir data [Finder ] data
  23. 23. (2) cd (Change Directory) tg02 $ cd [ $cd /Users/tg02/data $cd data] data
  24. 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. 25. (4) rmdir (ReMove DIRectory) $ rmdir UNIX
  26. 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. 27. DNA - (2):
  28. 28. 1958 Francis Crick (DNA) DNA RNA RNA replication transcription translation ( ) ( ) ( ) reverse transcription ( ) splicing ( ) RNA (non-coding RNA)
  29. 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. 30. (2): 5' 3'
  31. 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. 32. NCBI NCBI NCBI viewer query /keyword / / DDBJ/EMBL/GenBank (3): FASTA
  33. 33. NCBI http://www.ncbi.nlm.nih.gov/ NCBI National Center for Biotechnology Information (NIH) NLM National Library of Medicine 1 1988
  34. 34. NCBI Viewer query NCBI Search [All Databases] for [query] olfactory receptor NCBI query
  35. 35. NCBI Viewer keyword GenBank
  36. 36. NCBI Viewer [Display] [FASTA] DNA fasta [Send to] [Text] [FASTA], [Text] [File]
  37. 37. NCBI Viewer i) Accession number Search Nucleotide for Accession number ii) [Links] [Nucleotide] [Related Articles]
  38. 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. 39. (3): FASTA FASTA 1 1 '>' 2 2 (query) ( )
  40. 40. Ensembl Ensembl Ensembl viewer keyword Ensembl Gene Report 1,2 (4):
  41. 41. Ensembl http://www.ensembl.org/index.html Ensembl EMBL-EBI( ) Sangar Institute( ) 2000 NCBI ( )
  42. 42. Ensembl Viewer keyword
  43. 43. Ensembl Gene Report 1
  44. 44. Ensembl Gene Report Oligo Matches: microarray hit GO: Gene Ontology InterPro: InterPro Protein Family: Ensembl Trasncript structure: Protein features:
  45. 45. (4): 1 2 a b 1 2 (ortholog): (a1 a2 b1 b2) (paralog): (a1 b1 a2 b2 a1 b2 b1 a2)
  46. 46. Gene Report Export gene data
  47. 47. ContigView
  48. 48. Detailed View Ensembl Gene ID
  49. 49. Ensembl Viewer
  50. 50. Ensembl Viewer 1 BLAT GC 40% 45%
  51. 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. 52. (NCBI Ensembl) viewer

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