This document summarizes steps in a bioinformatics analysis pipeline involving BLAST, ClustalW, and SOAP. It describes running BLAST to identify sequences producing significant alignments to a query sequence and extracting identifier, name, and e-value information from BLAST results. It then discusses using ClustalW for multiple sequence alignment and SOAP for visualization of alignment and phylogenetic tree results. The document provides code snippets and filenames involved in steps for the analysis pipeline.

1. 20
DB
2008/08/11
kaneko.satoko(at)ocha.ac.jp

9. 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

10. Ensembl Syntenic region
Contig view View Syntenic regions

11. Figure
Figure

13. mouse vs. rat

15.
Ruby, Perl Python, Java 4
Ruby

16. ( )
h+p://togodb.dbcls.jp/togows_domes;c_method

17. Reverse strand 12.29kb

24. 3)SHH OMIM number KEGG ID

27. E-value
alignment
Swissprot ID

31. OUTORDER
Alignment aligned
aligned Alignment
input

32. CLUSTALW
alignment
Courier

38. BLAST clustalw
- blast_clustalw.rb 27 47 84

40.
- 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]

41. 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

43. Step50.rb clustalw SOAP
# SOAP CLUSTALW

44. blast_clustalw.rb 77-97 Step10-60
hsa:6469

46. Treeview dnd result
alignment
File→New
dnd