090622_blast-clustalw

2009/06/22 kaneko.satoko(at)ocha.ac.jp

BLAST CLUSTALW TogoWS REST SOAP (step ) (11):E‐value

(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

(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

(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

(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 #

# # 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

: 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]

(11):E‐value (ex. 0.0, e‐100 ) query E‐value query ‐ *E‐value *

(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 #

# # # 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

(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 #

# # 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

(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

(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

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

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090622_blast-clustalw

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