NCBI????????????????

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NCBI????????????????

• GenBank Overview
• ?????????
• ????????

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???GenBank?

• GenBank????13???,???100,000???????????????????????
  ?(CDS)?????,??????????GenBank????????????????,??EM
  BL?DDBJ?

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????

• ??GenBank??????????,???Entrez??????????

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??GenBank

• ??Entrez Nucleotides????
• ?accession number,????,??,??/????,???????????????
• ??Entrez??????????
• ?BLAST??GenBank????????????????
• ?E-mail???Entrez?BLAST????Query?BLAST?????????????
  ?FTP?????GenBank??????

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????

• ???????2.2.6(???????),2.2.7(???????),2.2.8(GenBan
  k??)???

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 ????

• ?? - ?????????,GenBank???,??????,GenBank????
•  ? - ????,?????????
•  ???? - 15?????????????GenBank???????????????

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 ?GenBank????

•  ????????,??accession number,?????????????
• BankIt - ??????????????WWW????????(??????VecScreen
  ????)

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 Sequin

• ??????,????????????,???,?????,alignments,??/??/??
  ??????
• ??????,?????TCP/IP?network aware??,???????NCBI??
  ??????Entrez?PowerBLAST?(??????VecScreen????)
•  ESTs - ??????,?????(??)???cDNA??????????????RACE?
  ??cDNA???

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GSSs

• ???????,?????(??)???cDNA??,exon
  trap?????,cosmid/BAC/YAC??,????
•  HTGs - ???????????????????,????(??0,1,2)????(??3)
  ???
• ????????HTG???????GenBank?Human Genome
  Sequencing??????

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 STSs ??????

• ?????????????????,?????????
•  ?SNPs - ????????????????????NCBI?????????????(db
  SNP)?

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

•  GenBank,DDBJ,EMBL - ???????,??????????
• GenBank,DDBJ(DNA Data Bank of Japan),and EMBL
  (European Molecular Biology Laboratory)???????????
  ????,?????????
• ??????????????????,??accession number,????????????
  ????,????accession number U12345?GenBank,DDBJ?EMBL
  ???????,???????????????,???????

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  DDBJ/EMBJ/GenBank???(???)

• ????????????????????????,??????????,??????????????
  ??????,??IUPAC??????????????
• FTP GenBank and Daily Updates

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GenBank??????

• ??GenBank??????GenBank??????????,????????????????
  ??????????
•  ASN.1?? ??????1,??????(ISO)??????,?????????????
  ?????????????

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 FASTA??

• ????????????(??),????????readme??,
• ??nt.Z(????????BLAST?????,
• ??GenBankEMBLDDBJPDB??,
• ???EST, STS, GSS, or HTGS??),nr.Z(???????????),est
  .Z, gss.Z, htg.Z, sts.Z,??????

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 ???????

• ????
•  Entrez?? ?accession number,????,??,??/????,????
  ????????????????(?GenBank PDB?)??????Entrez?????
  ??????????,????Batch Entrez(??Entrez)?
•  

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RefSeq

• NCBI????????????,?????,?????DNA
  contigs,?????mRNAs???,???,???????
• Accession numbers?NT_xxxxxx, NM_xxxxxx,
  NP_xxxxxx, ?NC_xxxxxx???????
•  dbEST ?????????,?????(??)???cDNA??????????????R
  ACE???cDNA???
•  dbGSS ???????????,?????(??)???cDNA??,exon
  trap?????,cosmid/BAC/YAC??,????

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 dbSTS

• ??????????,?????????????????,?????????
•  
• dbSNP ??????????,??SNPs,??????/??,??????,???????
  

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 ??????

•  ????Genome?Maps??,????????,?,??,??,??,??,???,??,?
  ?,viroids,???
•  ???

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UniGene

• ??????EST???mRNA??,????????????????????,??????????
  ???????????????????cluster???Unigene????,????????F
  TP??repository/UniGene??????
• ??UniGene
• ??UniGene
• ??UniGene
• ???UniGene

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BLAST

• ????????????????,????????(?????????Tools/Sequence?
  ?????)
•   BLAST ??
• BLAST??

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????

• Entrez?? ?accession number,????,??,??/????,??????
  ??????????????(?GenPept Swiss-Prot PIR RPF
  PDB?)??????Entrez???????????????,????Batch
  Entrez(??Entrez)?
•  

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RefSeq

• NCBI?????????Curated, ??????????DNA
  contigs,?????mRNAs???,???,???????Accession
  numbers?NT_xxxxxx, NM_xxxxxx, NP_xxxxxx,
  ?NC_xxxxxx???????

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 FTPGenPept

• ??genpept.fsa.Z??,????????GenBank/EMBL/DDBJ?????
  ???FASTA????????,??????????CDS??????
•  

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?????

• ????Genome?Maps??,????????,?,??,??,??,??,???,??,??
  ,viroids,???

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 Entrez???

• ????????????????????(TaxTable)????????????????????
  ,??????FASTA???BLAST?????????BLAST?????,?????????,
  ???????????????????????(????'Genomes?Maps,'??Entre
  z????????)
•  

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FTP?????

• ?ftp???genbank/genomes??????????FASTA????????.faa
  ??????.ptt???readme??????????Entrez???????
•  

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PROW

• Web??????,????200????CD??????????????????,???CD???
  ???20????????(????,??,??)
•  

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BLAST

• ????????????????,????????(?????????Tools/Sequence?
  ?????)
• BLASTp ??
• PSI-BLAST

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??

•  
• ???? ??NCBI?????????????????,??????????????(MMDB
  )????????????????
•  

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MMDB???????

• ????????????????,?????X-ray?????NMR?????
• MMDB????Brookhaven?????(PDB)????????,??????????MMD
  B????????????,????????????????????????????????????
  ?????,??????????????,?????????????????,??,????????
  ??,MMDB???????????????????????????

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MMDB

• MMDB????ASN.1????,???Cn3D, Rasmol, ?
  Kinemage??????,?????????????VAST??,???????VASTsear
  ch??????????
•  

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Cn3D

• See in 3-D, ????NCBI???????????????,?????3-D???
  ??????????????Cn3D??????????????????
•  

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VAST

• ??????????
• ???NCBI???????,????????????????????????????????,
  ??????MMDB????????????????????????????????????????
  ?
•  VAST ?? ?????????????????????????MMDB/PDB?????
  ????????VAST????????????????????,????????????????
  
•  

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???

• NCBI???????? ???????????,????????NCBI???????????
  ?????
•  ????? ??NCBI??????,????70000?????????,?????????
  ???????????????????????????????(??,?)???,??,??????
  ??????????????????,????????(??)?????NCBI??????????
  ?????????????????????
• ??? 

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???????

•  PubMed ???????????????,????,??,????????????????
  ?????NCBI?????????????????????URLs?
• PubMed??MEDLINE?PREMEDLINE?????????????MEDLINE????
  ????????,(???????)????????????????????PubMed??MEDL
  INE???????
•  

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?????

• ?????????PubMed????????,MEDLINE???,?ISSN???
•  PubRef(???) ?????????????????????,?????????????
• PubRef???PubMEd,?????????????????????????????PubMe
  d????????????????NAS??????????????????????
•  

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PubMed??(???)

• PubMed?????????NIH??,???????????????????????2000??
  ?????????????PubMed?????????????????????????????,?
  ??????????3?????????????????????????
•   PubMed

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OMIM?????????

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

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??

• ????????NCBI?????????,???????PubMed??????????????
  ?PubMed??????,??????????PubMed???????????????????
  
•  Molecular Biology of the Cell, 3rd ed. Alberts
  B., Bray D., Lewis J., Raff M., Roberts K.,
  Watson J.D., 1994, Garland Publishing.
•  

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????

• ??????,??????Entrez???????,??,???????????????????
  ????URL,????,????????????,????NCBI????????????????
  ?????????????Entrez?????????,?????????????????????
  ?NCBI PubMed????????NCBI?????(???)??????????????
  ???????
•  

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????

• ??????????PubMed????????PubMed ID?MEDLINE
  UID,??????(??,?,???)?
•  ??????????
• ????????????
•  E-mail?????????,??????????????????????,?citation_
  matcher_at_ncbi.nlm.nih.gov????????HELP?E-Mail?

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Genomes and Maps Overview

•  Entrez???(????)
•  Entrez??? ??800??GenBank?????????,????500???,gt2
  5???,??,???viroids,??,?????????????????,???,??,??,
  ???,??,?????,??,????????????/????????,????????????
  ???????????NCBI??????????????????TaxTables?

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Entrez Map Viewer

• Entrez????????????,???????(??????????)???(?????,??
  ??,??,????,?????)??????????
•  ???????Entrez????????lt350kb?????
•  ??NCBI ftp?????gt350kb???????genbank/genomes????r
  eadme??,ftp????????Entrez?????????
•  http//www.ncbi.nlm.nih.gov/Sitemap/index.html

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??

• ???????????????????????????????????????