PCR ????

1
????????????
2
????

• ?. ????????
• ?. ??????????????
• ??????????????,??????,??????
• ????????????,????????????????????????
• ??????????
• ?????????????????
• ????????

3

• ???????????????
• PCR ????
• DNA????????????????
• Contig Express----DNA ??????
• DNA ????
• ?????????
• ???????

4
?. ????????
5
????????

• ???????????????,????????????????,???????
  ???????????????????,???????????????

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?. ??????????????
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???????????

1. ??????????????,??????,??????
2. ????????????,????????????????????????
3. ??????????
4. ???????????????
5. ????????????(????,??????????)

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??1. ??????????????,??????,??????

• ?????????,???????,??????,????(Motif)?????????????
  ??????????(ORF),?????(CDS)???????RNA???????DNA????
  ?
• ?????????,??????(??Motif,?????,?????????,????????
  ??????????),????????????
• ????????????,????

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????????(????)

• http//www.labonweb.com IRACE (??????)
• BLAST??????
• ENTREZ SYSTEM (????????)

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ENTREZ ???????
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Vector NTI Suit ???????
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Vector NTI Suit ???????
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Antheprot 5.0 Dot Plot ???
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Peptool Lite--- Dot Plot ???
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DNASIS 2.5 ????????
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DNASIS 2.5 RNA ??????
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DNASIS 2.5 tRNA ??????
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RNAStructure 3.5 RNA ?????
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Omiga 2.0 ORF Map
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DnaStar ? Protean ???????????helical wheel ?
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??2. ????????????,????????????????????????

• ?????PCR??,?????????,??????,????,???????,
  ?????????????????????????????????????,???????????

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Vector NTI Suit 5.5 ????
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Gene Construction Kit 2.0 ????
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Winplas 2.6 ????
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OLIGO 5.0 PCR ????
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Atheprot 5.0 ????????
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Antheprot 5.0 ????????
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??3. ????????????????

• ????????,???????
• ?????????????(?ENTREZ?????????????????EndNote
  ??Reference Manager ????)????????
• ?? EndNote, Reference Manager

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Reference Manager 9 ??
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??4. ????????????????

• ?CDS(Coding Sequence)??????????????90??
• ????????????????
• PWM(??????)??
• ?????????,???????????????????????????????????????
  ???????,??????????????????????????

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DNASIS 2.5 ?????????A. (Codon Bias)
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DNASIS 2.5 ?????????B. (Rare Codon)
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DNASIS 2.5 ?????????C. (ORF List)
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DNASTAR ? GeneQuest ??CDS
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??5.????????

• ??????????,?????PDB?MMDB??????????????????????????
  ?
• X??????????????????????????????????,??????????????
  ??????????????,????????3??????????????????????????
  ??
• ????????????????????,????????????

36
???????????????

• ????(??????????)
• ????????(DALI??)
• ????????????
• ?????(fold recognition)
• ??????????????(fold
  library),????????????????,????????????,??????(th
  reading, sequence-structure alignment)
  ,??????(sequence-structure fitness alignment)
  ?????????????,????????????????????????????????????
  ??

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Cn3D 2.5 ?? 1EQF A?????
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RasMol 2.7 ??1EQF A?????
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PDB?MMDB?????
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?. ???????????????
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PCR ????
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???????

•   ????????????,?????????????????????????,??
  ????????????????DNA????(???)?

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• ?????????,????????????,?????(primer
  length),????(product length),??Tm? (melting
  temperature),?G?(internal stability),??????????(du
  plex formation and hairpin),??????(false priming
  site),?????GC??(composition),???????????,????????,
  ??????

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??????

• ????????16-23bp,??????18-21bp,??????????
• ??3????????A,??A?????????????????,???????????????
  ?????
• ???GC?????45-55,????????????????????GC?????????
• ??????????Tm????72???,????????????????Tm????????,?
  ???????????

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• ?G????????????????,?????????????,?????,?Oligo
  5.0????G????,????G??????????,?5???????G???,?3??G
  ?????,?????9(?G????,??????),??????????????????????
  ????,???????????????,???????????????,??5???????G?
  ???,?3??G???DNA??????DNA???,???????????

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• ?????????????????????????????,???????????,????????
  ??????100,??????????,?????????????????
• ???????????????????4.5,?????????????????????????PC
  R?????????
• ???????????????,???????????????,??????????????????
  ???????,??????????

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??????????????

• ??????????
• Primer Premier 5.0
• ??????????
• Oligo 5/6

gt gt gt gt gt
??????
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DNA????????????????
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???????

• ???????????????,??????????????????????????????????
  
• ? Dot Plot (??????)
• ?????????????????????????????????,???????
• ? Alignment (?????)

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????

• ?????
• Peptool Lite
• ?????
• Vector NTI Suit 6---AlignX

gt gt gt gt gt
??????
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Contig Express----DNA ??????
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????

• DNA??????
• Vector NTI Suit 6---ContigExpress Project

gt gt gt gt gt
??????
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DNA ????
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????

• DNA??????????????,
• ???????????????

gt gt gt gt gt
??????
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?????????
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?????

• NCBI (??)
• http//www.ncbi.nlm.nih.gov
• DDBJ (??)
• http//www.ddbj.nig.ac.jp
• EBI (??)
• http//www.ebi.ac.uk/index.html

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???????

• ????????(SGD)
• ????????(YPD)
• ??????(AtDB)
• ?????(OMIM)
• ?????(ACEDB)

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?. ???????
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????

1. PCR??????????????????
2. DNA,???????????????
3. ????????????????????

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1. ?????????,???,???,????,????????Dot Plot??
2. ???????????
3. ?????????????????????

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1. ???????????????????????
2. ???????????????(??????),Blastn/Blastp,NCBI
   Entrez??(????),????SNIP???
3. ???????????(??????????????,?????,????????????????)
   

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Thanks!