100603_TogoWS_SOAP

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100603_TogoWS_SOAP

  1. 1. 2010/06/03   kaneko.satoko(at)ocha.ac.jp   
  2. 2. (FTP )  KEGG  TogoWS SOAP 
  3. 3. FTP $lCp Cp://Cp.ensembl.org/pub/current_fasta/  #   lCp> ls  #   lCp> cd raNus_norvegicus  lCp> ls  #   lCp> cd dna  lCp> ls  # ( dna, dna_rm 2 )  lCp> mget  RaNus_norvegicus.RGSC3.4.58.dna.chromosome.7.fa.gz  lCp>quit  *dna_rm repeat mask
  4. 4. KEGG hNp://www.kegg.jp/ja/  KEGG Kyoto Encyclopedia of Genes and Genomes   KEGG     LinkDB              hNp://www.genome.jp/kegg/kegg1a_ja.html  KEGG       PATHWAY   BRITE    
  5. 5. KEGG query query Search KEGG   KEGG DGENES: 
  6. 6. KEGG query   (Mus musculus, mmu) Makorin1   Makorin1 BRITE hierarchy 2   : Homo sapiens → hsa      Mus musculus → mmu
  7. 7. KEGG query   moff   4 1     View moffs   hit  
  8. 8. KEGG query Ortholog, Paralog  Ortholog Paralog query moff   CLUSTALW, MAFFT, PRRN ‐>  alignment  Draw alignment ‐> alignment   Search common moffs ‐> moff   List definifon ‐>   ‐> alignment fasta  
  9. 9. Olr1082 query olfactory receptor gene PATHWAY    
  10. 10. PATH:rno04740     odorant( )  ↓  Golf (G protein)  ↓  AC (adenylate cyclase)  ↓  cAMP  ↓  CNG (cyclic nucleofde gated channel)    ↓    Ca2+  ↓  CLCA (chloride channel calcium acfvated)
  11. 11. KEGG REST   hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484  hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/   # ID  hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/division  #   hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/organism    #   hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/gene  #   hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/definifon  #   hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/posifon  #   hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/aaseq  #   hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/aalen  #   hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/ntseq  #   hNp://togows.dbcls.jp/entry/kegg‐genes/mmu:54484/ntlen  #   KEGG ORTHOLOGY   kegg‐ /K04257  kegg‐ /K04257/   # ID kegg‐ /K04257/   #KO kegg‐ /K04257/     #   kegg‐ /K04257/pathways  #pathway kegg‐ /K04257/   #KO class
  12. 12. TogoWS: REST  Database search  ‐ ‐ REST ID   ID     hNp://togows.dbcls.jp/search/ncbi‐omim/olfactory  hNp://togows.dbcls.jp/search/ncbi‐omim/makorin  hNp://togows.dbcls.jp/search/ncbi‐omim/carboxylesterase  hNp://togows.dbcls.jp/search/ebi‐biomodels/olfactory  hNp://togows.dbcls.jp/search/ebi‐go/carboxylesterase  hNp://togows.dbcls.jp/search/ebi‐go/olfactory  hNp://togows.dbcls.jp/search/kegg‐enzyme/carboxylesterase  hNp://togows.dbcls.jp/search/kegg‐reacfon/carboxylesterase  hNp://togows.dbcls.jp/search/kegg‐pathway/olfactory  hNp://togows.dbcls.jp/search/ncbi‐cdd/carboxylesterase        (cdd: conserved domain database) 
  13. 13. OMIM       ( 12 )   OMIM   science writer     6   1‐‐‐‐‐ (100000‐ ), 2‐‐‐‐‐ (200000‐ ): Autosomal loci or phenotypes   (entries created before May 15, 1994)  3‐‐‐‐‐ (300000‐ ): X‐linked loci or phenotypes  4‐‐‐‐‐ (400000‐ ): Y‐linked loci or phenotypes  5‐‐‐‐‐ (500000‐ ): Mitochondrial loci or phenotypes  6‐‐‐‐‐ (600000‐ ): Autosomal loci or phenotypes (entries created aCer May 15, 1994) 
  14. 14. Togo WS SOAP TogoWS SOAP CLUSTALW   BLAST CLUSTALW SOAP  
  15. 15. TogoWS SOAP         Ruby, Perl Python, Java 4     Ruby  
  16. 16. ( ) hNp://togodb.dbcls.jp/ws_service 
  17. 17.     Sonic Hedgehog’ query     Sonic Hedgehog   hedgehog hedgehog   hedgehog homolog   (Echelard et al. 1993 Cell. 75:1417‐1430.)  Sonic Hedgehog (SHH)  3 exons,   CDS 1389bp (462a.a.) 
  18. 18. 1)  REST   2)  query (BLAST)   3)   4)  CLUSTALW alignment   CLUSTALW BLAST sequencer alignment   CLUSTALW alignment (mulfple alignment)   matrix alignment  
  19. 19. SOAP   [database ]     CotEditor Macintosh HD/ /tg03/bin     $cd bin  $ruby [ .rb]
  20. 20. 1)  SHH REST     hNp://togows.dbcls.jp/search/ebi‐uniprot/sonic+hedgehog+human  hNp://togows.dbcls.jp/entry/ebi‐uniprot/SHH_HUMAN.fasta  CotEditor Macintosh HD/ /tg03/ bin shh_human.txt   KEGG   hNp://togows.dbcls.jp/search/kegg‐genes/shh  hNp://togows.dbcls.jp/entry/kegg‐genes/hsa:6469/aaseq 
  21. 21. 2) Sonic Hedgehog query        BLAST   DdbjBlastSearchSimple.rb  (SOAP )  [SHH ] #   blast_shh  
  22. 22. BLAST   E‐value     alignment   Swissprot ID
  23. 23. 3)  Sonic Hedgehog       DdbjGetentryGetSwissProtEntry.rb  #!/usr/bin/env ruby  require 'soap/wsdlDriver'  wsdl = "hNp://togows.dbcls.jp/soap/wsdl/ddbj_getentry.wsdl"  serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver  accession = "Q62226"  result = serv.DdbjGetentryGetSwissProtEntry(accession)  puts result  #   shh_mouse  
  24. 24.   REST   hNp://togows.dbcls.jp/entry/ebi‐uniprot/Q62226.fasta 
  25. 25. 4) CLUSTALW alignment   DdbjClustalwAnalyzeParam.rb  #!/usr/bin/env ruby  require 'soap/wsdlDriver'  wsdl = "hNp://togows.dbcls.jp/soap/wsdl/ddbj_clustalw.wsdl"  serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver  query = <<QUERY  > human‐shh   [ ]  > mouse‐shh   [ ]  > rat-shh [ ]  QUERY  param = "‐align ‐matrix=blosum ‐gapdist=8 ‐maxdiv=40 ‐outorder=aligned ‐pwmatrix=blosum"  result = serv.DdbjClustalwAnalyzeParam(query,param)  puts result  shh_align  
  26. 26. CLUSTALW   param = "‐align ‐matrix=blosum ‐gapdist=8 ‐maxdiv=40 ‐outorder=aligned ‐pwmatrix=blosum"  MATRIX     L U mulfple alignment   OUTORDER  Alignment   aligned    aligned  Alignment    input    BLOSUM     hNp://www.ddbj.nig.ac.jp/search/help/clustalw_help.html 
  27. 27. CLUSTALW   alignment     Courier
  28. 28.  Makorin1 mulfple alignment   1) REST Makorin1   2)  query BLAST   3) BLAST   4) BLAST 8 CLUSTALW alignment  
  29. 29.  KEGG    TogoWS SOAP   TogoWS REST SOAP    

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