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090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
090622_blast-clustalw
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090622_blast-clustalw

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  • 1. 2009/06/22   kaneko.satoko(at)ocha.ac.jp   
  • 2. BLAST CLUSTALW   TogoWS REST SOAP  (step )  (11):E‐value  
  • 3. (1)   blast_clustalw.rb    blast_clustalw.rb    $ ruby blast_clustalw.rb hsa:6469  (  has:6469 blast + clustalw     blast_clustalw.rb      step10.rb   step20.rb Blastp   step30.rb Blastp ID E‐value   step40.rb ID E‐value  E‐value   step50.rb   step60.rb ClustalW mulSple alignment  
  • 4. (2) step10.rb k.step10.txt    ‐ hsa:6469 ( ID kegg_id )  ‐blast_clustalw.rb 8‐12 get_aaseq   ‐  last_clustalw.rb b get_aaseq 79   #!/usr/bin/env ruby  require ‘open‐uri’ # 8 open URL REST   #  kegg_id  kegg_id = "hsa:6469";   #  kegg_id  aaseq  aaseq = open("hap://togows.dbcls.jp/entry/gene/" + kegg_id + "/aaseq").read   #REST hap://togows.dbcls.jp/entry/gene/has:6469/aaseq  # aaseq    #  aaseq  k.step10.txt  out = open("k.step10.txt","w")  out.puts aaseq  out.close 
  • 5. (3) step20.rb   Sonic Hedgehog query BLAST   ‐blast_clustalw.rb 15‐25   ‐ blast_clustalw.rb 81   #!/usr/bin/env ruby  require 'soap/wsdlDriver'  # step10.rb aaseq  aaseq = File.read("k.step10.txt”)  # blast  result_blast  wsdl_blast = "hap://togows.dbcls.jp/soap/wsdl/ddbj_blast.wsdl"  serv_blast = SOAP::WSDLDriverFactory.new(wsdl_blast).create_rpc_driver  program    = "blastp"  database   = "SWISS"  result_blast = serv_blast.DdbjBlastSearchSimple(program,database,aaseq)  # ↑SOAP blast   # result_blast  k.step20.txt  out = open("k.step20.txt","w")  out.puts result_blast  out.close
  • 6. (4) step30.rb  BLAST clustalw   ‐ blast_clustalw.rb  27 47 84   #!/usr/bin/env ruby  require 'soap/wsdlDriver'  #  step20.rb blast  result_blast  result_blast = File.read("k.step20.txt")  # result_blast  spid_hash  #  spid_hash = Hash.new #    # blast  line  result_blast.each_line do |line|    # blast sp  if line =~ /^sp|(.+)|(.+)s+.+s+[0‐9]+s+(.+)$/      spid = $1      #  spid  spname = $2    #  spname  evalue = $3    #  evalue  if evalue =~ /^e/ #  evalue  e   evalue = “1.0” + evalue #  1.0       end  #   
  • 7. #     # evalue  evalue_float  evalue_float = evalue.to_f      # spid_hash[spid]  spname  evalue_float  spid_hash[spid] = {:name=>spname, :evalue=>evalue_float}    end  end  #  spid_hash  k.step30.txt  #  out = open("k.step30.txt","w");   spid_hash.each {|spid,value|    out.prinv("%s|%s|%sn",spid,value[:name],value[:evalue]);   }  out.close step20 blast k.step20.txt  ID e‐value   k.step30.txt     ‐ hsa:6469 ( ID kegg_id )  ‐blast_clustalw.rb 28‐47 parse_blast   ‐  last_clustalw.rb b get_aaseq 84  
  • 8. : step30.rb   ‐ if line =~ /^sp|(.+)|(.+)s+.+s+[0‐9]+s+(.+)$/   BLAST 1     ‐ f  I if )   spid spname evalue    .:  , +:  1 , s:  , $:    ():  , []: []   Score E Sequences producing significant alignments: (bits) Value sp|Q15465|SHH_HUMAN Sonic hedgehog... 720 0.0 sp|Q62226|SHH_MOUSE Sonic hedgehog... 682 0.0 sp|Q63673|SHH_RAT Sonic hedgehog... 679 0.0 sp|Q91035|SHH_CHICK Sonic hedgehog... 605 e-172 sp|Q90385|SHH_CYNPY Sonic hedgehog... 510 e-144 spid spname evalue spid_hash[spid][:name] spid_hash[spid][:evalue]
  • 9. (11):E‐value   (ex. 0.0, e‐100 )    query E‐value query   ‐    *E‐value     *  
  • 10. (5) step40.rb Blast E‐value   Step30 k.step30.txt  E‐value   k.step40.txt   ‐ hsa:6469 ( ID kegg_id )  ‐blast_clustalw.rb 39‐43   ‐blast_clustalw.rb e‐value 6   #!/usr/bin/env ruby  #  min_evalue = 1e‐170  # step30.rb   #  spid_hash  lns_spid = File.read("k.step30.txt")  spid_hash = Hash.new  lns_spid.each_line do |line|    raise unless line =~ /^(.+)|(.+)|(.+)$/    spid = $1    spname = $2    evalue = $3    spid_hash[spid] =     {:name=>spname, :evalue=>evalue.to_f}  end #   
  • 11. # #  #  spid_hash.each {|spid,value|    #  if value[:evalue] > min_evalue then      spid_hash.delete(spid)   #  end           }  #  k.step40.txt  out = open("k.step40.txt","w");   spid_hash.each {|spid,value|    out.prinv("%s|%s|%sn",     spid,value[:name],value[:evalue]);   }  out.close 
  • 12. (6) step50.rb  Sonic Hedgehog   ‐ blast_clustalw.rb  49 59 87   #!/usr/bin/env ruby  require 'open‐uri’  #    #  spid_hash  lns_spid = File.read("k.step40.txt")  spid_hash = Hash.new  lns_spid.each_line do |line|    raise unless line =~ /^(.+)|(.+)|(.+)$/    spid = $1    spname = $2    evalue = $3    spid_hash[spid] = {:name=>spname, :evalue=>evalue.to_f}  end  #   
  • 13. # #  spid_hash  spid_hash.each {|spid,value|    #  uri = "hap://togows.dbcls.jp/entry/uniprot/" + spid + "/seq”  # REST     value[:seq] = open(uri).read  }  #  fasta  out = open("k.step50.fa","w");   spid_hash.each {|spid,value|    out.prinv(">%s|%s|%sn",spid,value[:name],value[:evalue]);     out.prinv("%sn",value[:seq]);   }  out.close 
  • 14. (7) step60.rb  CLUSTALW alignment   Step50.rb  clustalw  SOAP   ‐ blast_clustalw.rb  61 75 90   #!/usr/bin/env ruby  require 'soap/wsdlDriver’  # fasta  query  query           = File.read("k.step50.fa")  # query  mulSple alignment wsdl_clustalw   = "hap://togows.dbcls.jp/soap/wsdl/ddbj_clustalw.wsdl"  serv_clustalw   = SOAP::WSDLDriverFactory.new(wsdl_clustalw).create_rpc_driver  param           = "‐align ‐matrix=blosum ‐gapdist=8 ‐maxdiv=40 ‐outorder=aligned ‐ pwmatrix=blosum”  # SOAP CLUSTALW   result_clustalw = serv_clustalw.DdbjClustalwAnalyzeParam(query,param)  #  k.step60.txt  out = open("k.step60.txt","w");   out.puts result_clustalw out.close
  • 15. (8) blast_clustalw.rb   blast_clustalw.rb  77‐97 Step10‐60   shiz    # ID hsa:6469 # step10.rb    # step20.rb  #step30.rb step40.rb  #step50.rb  #step60.rb  #  auto.txt 
  • 16. blast_clustalw.rb   1)  hsa:6469 MIN_EVALUE ( 1.0e‐140, 1.0e‐120,   1.0e‐100 ) mulSple alignment ( )   2) rat Olr1082 mulSple alignment human mouse   ortholog   ‐    rat Olr1082 UniProt ID   REST Entry retrieval UniProt KEGG ID   blast_clustalw.rb (MIN_EVALUE 1.0e‐100)  mulSple alignment ortholog   Ensembl Synteny ortholog
  • 17. SOAP REST      

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