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080812

  1. 1. 20 DB 2008/08/12 kaneko.satoko(at)ocha.ac.jp
  2. 2. ATGC Figure Figure 4-5 Molecular Biology of the Cell (© Garland Science 2008)
  3. 3. 3% junk DNA junk DNA Figure Figure 4-17 Molecular Biology of the Cell (© Garland Science 2008)
  4. 4. C α T β β β β A T Figure α A G α :transition β :transversion G C purine pyrimidine Figure 4‐4  Molecular Biology of the Cell (© Garland Science 2008) 
  5. 5. (polymorphism) (substitution) 1 (mutation) (advantageous) (neutral) (deleterious)
  6. 6. ( ) ( ) 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·
  7. 7. TCAGTGACCT TCTGTCACGT TCTGTGACCT 6th G C 3th T A 9th C G TCAGTGACCT TCTGTCACGT
  8. 8. ATGC 4 1 2 TCTGAGACCT TCTGTGACCT 5th A T 6th G C 3th T A 6th G C 6th G C 3th T A 9th C G 9th C G 5th A T 6th C G TCAGTGACCT TCTGTCACGT TCAGTGACCT TCTGTCACGT Jukes and Cantor (1969) Kimura 2-parameter(1980)
  9. 9. Coding Sequence 2
  10. 10. 1st (Leu, Arg) 2nd 3rd transition
  11. 11. synonymous substitution S nonsynonymous substitution N a) TCA TCT Ser a) T Ser 2 C Ser 0/2 1/1 3 A T Ser N S b) c) b) Leu Arg 6 1 ( ) c) 0/1 2/2 / N S
  12. 12. 2 ( ) d) 1/4 CAT CGG 1/4 2 N N CGT CAG 2 4 1/4 1/4 S N d) 1/4x2=0.5 1( 1 )+3/4x2=2.5 e) f) e) 1/4 1/4 1/4 1/4 (1/4+1/4)x2=1 N S N N 1( 2 )+ (1/4+1/4)x2=2 1/4 1/4 1/4 1/4 f) S N N N
  13. 13. [] S N
  14. 14. [] S N 6
  15. 15. ( ) 2 a) b) c)
  16. 16. a) b) c) 1/4 1/4 1/4 1/4 1/4 1/4 S N N S N N 1/4 1/4 1/4 1/4 1/4 1/4 S N N N N S :(1/4+1/4)x2 = :0 (1/4+1/4)x2+1 = :3 :(1/4+1/4)x2 = (1/4+1/4)x2+1 =
  17. 17. NJ (Neighbor-Joining) MP (maximum parsimony) ML (maximum likelihood S.
  18. 18. seq1 seq2 seq3 seq4 seq1 2 seq2 0.2 seq3 seq4
  19. 19. seq1 seq2 seq3 seq4 seq1 seq2 0.2 seq3 0.1 0.3 seq4 0.4 0.4 0.5 seq1 0.1
  20. 20. seq1 seq2 seq3 seq4 seq1 seq2 0.2 seq3 0.1 0.3 seq4 0.4 0.4 0.5 seq2 (0.1) seq1 (0.1) (0.1) (0.3) seq3 seq4 0.1
  21. 21. seq1 seq2 seq3 seq4 seq5 seq6 seq1 seq2 0.2 seq3 0.1 0.3  seq4 0.3 0.3 0.4 seq5 0.2 0.4 0.3 0.5 seq6 0.2 0.4 0.3 0.5 0.2 seq1 0.1
  22. 22. seq1 seq2 seq3 seq4 seq5 seq6 seq1 seq2 0.2 seq3 0.1 0.3  seq4 0.3 0.3 0.4 seq5 0.2 0.4 0.3 0.5 seq6 0.2 0.4 0.3 0.5 0.2 seq6 seq5 (0.1) seq2 (0.1) (0.1) seq1 (0.1) (0.1) (0.1) (0.2) seq3 seq4 0.1
  23. 23. 1 2
  24. 24. 3 4
  25. 25. node
  26. 26. 3
  27. 27. -Rhodopsin - Forward strand 6.70kb
  28. 28. CLC Sequence Viewer CLC Sequence Viewer (Free) http://www.clcbio.com/index.php?id=910 Installer Installer( )
  29. 29. CLC Sequence Viewer CLC Sequence Viewer 5 Plug-ins and Resources Download Plug-ins Additional Alignments ClustalW
  30. 30. CLC Sequence Viewer ClustalW CLC_Data Rhodopsin
  31. 31. NCBI Search NCBI [All Fields] [Definition/Title] Rhodopsin Add search parameter [Organism] human human NM_000539, chimpanzee XM_516740, rhesus monkey XM_001094250
  32. 32. Download and Save OK Accession number
  33. 33. Annotation layout Show annotation Annotatioin types CDS CDS Delete Selection
  34. 34. ClustalW alignment Tool box Additional Alignment ClustalW alignment Next parameter Gaps Custom gap open penalty Make a phylogenetic tree( ) alignment check Finish
  35. 35. Gap penalty
  36. 36. Alignment alignment (human, chimpanzee, rhesus monkey )
  37. 37. [.aln] Export Format Clustal Alignment (.aln) alignment Export
  38. 38. transition/transversion Rhodopsin CDS(coding sequence) 1047bp transition: A G, C T transversion: A,G C,T human – chimpanzee, human – macaque (NM_000539)-(XM_516740) (NM_000539)-(XM_001094250) transition transversion p-distace p-distance = / transi?on transversion p‐distance (%) human‐ chimpanzee human‐  macaque 
  39. 39. Rhodopsin CDS(coding sequence) 1047bp transition: A G, C T transversion: A,G C,T human – chimpanzee, human – macaque (NM_000539)-(XM_516740) (NM_000539)-(XM_001094250) transition transversion transi?on transversion p‐distance (%) human‐ 5 1 6/1047 = 0.5 chimpanzee human‐   31 9 40/1047 = 3.8 macaque 600 2500
  40. 40. Rhodopsin rhesus monkey rabbit harp seal manatee dolphin elephant dannart (Marsupial) platypus (Monotreme) NJ tree bootstrap distance:Modified Nei&Gojobori Nonsynonymous(p-distance) number of sites:738 cod finch
  41. 41. NCBI Accession number Search Nucleotide for Accession number Accession number
  42. 42. alignment Toolbox Create Tree alignment Next
  43. 43. ( ) Neighbor joining Bootstrap 1000 Bootstrap OTU
  44. 44. Rhodopsin alignment 1) / / 2) alignment insertion( ) deletion( ) 3) 4)
  45. 45. 20 DB

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