? ? ? ? ? Bioinformatics

1
? ? ? ? ?Bioinformatics

• ???? ? ? ?
• Bioscau_at_21cn.com

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?????

• ?yahoo.com.cn???????????????

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? ? ? ? ?

• ?????
• ??????????
• ??????????

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? ? ? ? ?

• ???????
• ?????????
• ?????????????????
• ????????????????
• ????????????????GenBank????????SWISS-PORT
  ????????? PDF???????????
• ???????????????????

5
?????????????????,??????

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

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1???

• ?????(Bioinformatics)?????????????????????????????
  ???????????????????????????????,??????????????????
  ?????????????????????,???????(HGP)????????????????
  ??

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2?????????????

• ????????,??????????,??????????????? (Post-genome
  Era) ???,?????????????????????????????,???????????
  ?????DNA??????????1.8????????,?1997??????1.2109bp
  ??????????????????????,???????????????????,???????
  ????,????????

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3??????????????

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

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4??????

• ?????????,???5-10???????????????????1985??????,???
  ??????30????????,????????????????????,??????????,?
  ??????????????????????1990?????,??30?????????,?30?
  ????????????????,??????????????????????????,??????
  ???????????????????,???????????????????,??????

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?????

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

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???????????

• ?????(Bioinformatics)----?????????????????????????
  ???????????????????(??????)???????????????????????
  ???????????????????????????????????????????????,??
  ????????????????,?????????????????????????????????
  ?,????????????????????????,???????????????????????
  ,????????????????????????

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??????????

• ??????????,???????
• ????????????????????????????????PC???
• ?????????????????????????????????????(Interface)
  
• ?????????????????????????????????????????????????
  ?????????????????????????????????????,???????????
  ??

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

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

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1?????

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

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2???????

• ??,??????????????,??????????????????????????,?????
  ?????????(National Center for Biotechnology
  Informatics,NCBI)??????????? (European
  Bioinformatic Institute,EBI)??????????(Center for
  Information Biology,CIB)??NCBI?EBI?CIB????,?????Ge
  nBank?EMBL?DDBJ???????????????????????????,???????
  ????????????,?????????????????

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3???????

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

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4??????????

• ??????????????????????????????????????????????????
  ??????????????????????????????????????????????????
  ????????????????????????????????????????(?????????
  ??????)???????????????????????????????????????????
  ?????????????????????????????????????????????????
  ???????????????????

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4??????????

• ??????????????????????????????????????????????????
  ??????????????????????????????????????????????????
  ????????????????(???????????????)?????????????????
  ???????????????????????????EMBL???????,???????????
  ?,??????????http//www.Ipc.pku.edu.cn/mirror/mirro
  r.htmlhttp//www.Ebi.pku.edu.cn)????????????????
  ?????????????????????????????????????????????????
  ??????????

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? ????

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

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1 ????????????

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

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2??????????

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

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???????

•  Genbank,????????????????(available at
  http//ncbi.nhm.nlm.gov)?
•  EMBL,???????????????? (available at
  http//www.embl-heidelberg.de)?
• DDBJ,???DNA?????(available at http//www.nig.ac.j
  p )?

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Genbank

• ????????????????
• ????????????http//www.gzsums.edu.cn/
• ??Entrez?????BLAST???????

24
?????????
25
???????

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

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 EMBL

• ???????????????????
• DDBJ,???DNA?????(available at http//www.nig.ac.j
  p )?

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???????

• PDB(available at http//www.ipc.pku.edu.cn/npdb
  )??
• ??????????????
• SCOP(available at http//www.ipc.pku.edu.cn/scop/
  )??
• ??????????
• OMIM(available at http//www3.ncbi.nlm.nih.gov/omi
  m/)?

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Helix-turn-helix motif of protein binding to DNA
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????????????

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

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3???????????????

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

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???????????

• ????????????????????????????,????????n??????m??,?
  ??????????????????????
• ???????????
•         

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???????????

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

33
???????????

• ??20?????,???????????????????????,????????????
  ?
• ????????????????
• ?????????????
• ??????????
• ????????

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4 ?????????????

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

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5 HGP???,?????????????

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

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6 ???????????,????????????

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

37
???????
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7 DNA?????????

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

39
????????
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?HGP???????????

• ???????????????????HGP,????????HGP??????????,??HGP
  ????????????????

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1)???????????????????

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

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80-99?Protein Data Bank http//www.rcsb.org/pdb/in
dex.html
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2)???????

• ??DNA?????????????500bp??????????????????DNA??????
  ?? ???????????????????????????????????????????????
  ?????????????????????????,????????????????????,???
  ?????????(redundancy,????????)???????????????

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3)???????

• ?????????,?????????DNA??,?????????????????????????
  ????,?????????????????????
• ?????????,??????DNA???????????,???????????????????
  ???????????????????????????????????????????????(?T
  ATA box?????)???,???????????

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(4)??????

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

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(5)???????

• ?????????????????????????????????????????????????,
  ?????????????????????????????????????,????????????
  ????????????????????????????,?????????????????????
  ?????????????????(Comparative Genomics)?????

47
????

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

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(1)????

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

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(2)?????????

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

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(3)???????????????????????

• ????,??????????????????,??????????????????????????
  ???????????????????????????????????????,??????????
  ??????????
• ?????????????????,????????????????,????"??"???????
  ??????????????????,???????????????????????????????
  ??????????,???????????????????????????,???????????
  ?

51
???????

• ???????,???????????,???????????????????,??????????
  ?????????????????????????????????,???????,????????
  ??????,???????????,??????????????????????????????
  ????????????????EST??,??????????????????????,?????
  ??????????????????????????????????????????????????
  ???????

52
????????????

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

53
????????????

• ????????????,?????????????????????????????????,???
  ??????????????????????????????????????????????????
  ??????????????,??????????????????????,????????????
  ???????????????????????????????????,??????????????
  ??????????????????????????,??????????????????WWW??
  ????????????? ????????????????,?????????????

54
??????????????????????(1)

• ????(Neural Networks)
• 1982?,??????????????????,??Stormo?????????????
  ????????????????????????1988?,??Qian and
  Sejnowski???????????????????,?????????????????????
  ????????,??????????,??????????????????????

55
??????????????????????(2)

• Threading??
• Threading?????????????,???????????????????????
  ??????????,???????????????????????????,???????????
  ??,?????????????????

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3?WWW??????????????????
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(1)????????

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

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Sequence

• DNA
• Genbank (www.ncbi.nlm.nih.gov)
• - Entrez
• - BLAST
• EMBL (European Molecular Biology Laboratory,
  www.ebi.ac.uk)
• - SRS srs.ebi.ac.uk , www.sanger.ac.uk/srs6/
• DDBJ (DNA Data Bank of Japan)

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2) ????????????

• BLAST(Basic Local Alignment Searching Tool)
• ??????retrieval system ???????????????EMBLGenbank
  DDBJ,???????????????????DNA?RNA?????,???????t-RNA
  ????HIV??????,????????????,?????????????????
• ?????????DNA??,??????????????,????????????

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3)????????????

• FASTA 96????FASTA3?????????,????CPU??????????????
  ,???????????(Parallel Virtual Machine),???????????
  ?
• ???????(Mulitple Alignment)(????????????)
• Clustalw,MAP,Pima?

61
4)??????????

• Mfold
• Mfold????RNA????????,????????????????,???????
  ?????????????????????,?????????
• RasmolRasmol www.umass.edu/microbio/rasmol/
• Mage,raster3D,Grasp?

62
 Introduction to Rasmol
63
5)???????????

• Procheck
• WHATIF
• DSSP

64
Protein classification databases

• Prosite (expasy.hcuge.ch)
• Pfam (www.sanger.ac.uk/Pfam)
• - Structure
• PDB(Protein Data Bank,) www.rcsb.org/pdb/cgi/query
  Form.cgi
• (RCSB, Research Collaboratory for Structural
  Bioinformatics, rcsb.rutgers.edu) Xray
  crystallography

65
Protein

• Protein
• explorer www.umass.edu/microbio/chime/explorer/
• Cn3D www.ncbi.nlm.nih.gov/Entrez
• SwissPDB
• Viewer
• expasy.proteome.org.au/spdbv/

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6)??????????

• GCG

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Managing the GCG environment

• - Moving files between the personal computer and
  the computer hosting GCG
• Tutorial for PC
• (For Mac make use of Fetch instead of CuteFTP)
• Use Word to create a short nucleotide sequence (
  about 20 bases) . Save this sequence in Word as a
  text file
• and under the name "my.seq". (Save as ... select
  Text format). Exit from Word and start CuteFTP
• CuteFTP In the FTP site manager "Add site".
• Site label whatever you want
• Host address bio.lundberg.gu.se
• User ID your GCG account name
• Password your GCG account password
• Click "OK".

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Connect

• Click "Connect" in the FTP site manager. Click OK
  in the window "login information". You're now
• connected to bio.lundberg.gu.se and the directory
  to the left is that of the PC and the directory
  to the right is
• that of bio.lundberg.gu.se. You can move files
  simply by double-clicking on them. Try to find
  the sequence
• you created on the PC. As you double-click on it,
  it will be transferred to bio.lundberg.gu.se.
  Quit CuteFTP
• and login to bio.lundberg.gu.se. Try "ls" to see
  if you're file has been transferred there.
  Finally use the
• reformat my.seq
• command to convert the sequence to GCG format.
  Use the command
• cat my.seq
• to see the result of the reformatting.
• Transfer of a file from GCG to the personal
  computer is done is the same way as described
  above, except that
• in CuteFTP you double-click on the GCG file to
  transfer it to the PC.

69
7)?????

• ???????????,??????????????????,???????????????????
  ,????????????Genebank?EMBL?DDBJ?Swiss-Port?PIR?PDB
  ??

70
???????????????????
71
???????????????

• ???????,??????????????????????????
• ??????????(??????????????),??????????????
• ????,????, ??, ????????????????
• ??????????,???????????????
• http//genome.zsu.edu.cn/

72
??????

• ??????????????,? ?????????????SWISS-PROT????????
  ????????????????????????????????????????(???)????
  ?????(??kb)????????
• ?????????????????,? ???????????????????????????
  ?????? ??

73
????????

• EBI?SRS(sequence retrieval system)????????????????
  ??
• PDB?3DBBROWSER,??????????,?????????FASTA???????,??
  ?????????????????????????VRML?,?????????????SCOP?C
  ATH?MEDLINE???? 3D??
• Rasmol www.umass.edu/microbio/rasmol/
• Weblab www.msi.com
• Kinemage www.cryst.bbk.ac.uk/PPS/vsns-pps/technolo
  gy/kinemage.html
• Chime www.umass.edu/microbio/rasmol/

74
??

• ???HGP??????????????????,???????????????,?????????
  ???????

75
5?????

• European Bioinformatics Institute EBI) 
• SBDS (Southampton Bioinformatics Data Server) 
• U.S. Department of Energy - Bioinformatics
  Infrastructure 
• The NASA Ames Center for Bioinformatics 
• The National Center for Biotechnology
  Information 
• Protein Data Bank (PDB)Mirror Site
• ???????????
• ????????
• BioSino?????? 

76
6.????

• ????? ??????? (2000-04-03 )
• ???????????? (2000-05-16 )
• ???????????????? (2000-05-17 )
• ?????????????????? (2000-06-29 )
• ????DNA????????? (2000-07-04 )
• ?????????????????? (2000-07-04)
• ?????????????????? (2000-07-05 )
• ??????????? (2000-07-16 )
• ?????????????????? (2000-07-19 )
• 2000????????????????? (2000-08-10)
• (???????????,2000?10?31?)