080811

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080811

  1. 1. 20 DB 2008/08/11 kaneko.satoko(at)ocha.ac.jp
  2. 2. Olr1082 40kb Olr1083 annotation Olr1082 2 2 1 2 3 4 1 4 Deletion 1 2 3 4 1 2 3 2 3 4 Duplication
  3. 3. Ensembl Syntenic region Contig view View Syntenic regions
  4. 4. Figure Figure
  5. 5. mouse vs. rat
  6. 6.   Ruby, Perl Python, Java 4 Ruby
  7. 7. ( ) h+p://togodb.dbcls.jp/togows_domes;c_method 
  8. 8. Reverse strand 12.29kb
  9. 9. 3)SHH OMIM number KEGG ID
  10. 10. E-value alignment Swissprot ID
  11. 11. OUTORDER Alignment aligned aligned Alignment input
  12. 12. CLUSTALW alignment Courier
  13. 13.
  14. 14. BLAST clustalw - blast_clustalw.rb 27 47 84
  15. 15.
  16. 16. 
 - if line =~ /^sp|(.+)|(.+)s+.+s+[0-9]+s+(.+)$/ BLAST 1 - f I if ) spid spname evalue -  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]
  17. 17. 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
  18. 18. Step50.rb clustalw SOAP # SOAP CLUSTALW
  19. 19. blast_clustalw.rb 77-97 Step10-60 hsa:6469
  20. 20. Treeview dnd result alignment     File→New dnd

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