1. 2010/06/03
kaneko.satoko(at)ocha.ac.jp

2. (FTP )
KEGG
TogoWS SOAP

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. 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. KEGG query
query Search KEGG
KEGG DGENES:

6. KEGG query
(Mus musculus, mmu) Makorin1
Makorin1
BRITE hierarchy
2
: Homo sapiens → hsa
Mus musculus → mmu

7. KEGG query
moff
4 1
View moffs
hit

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. Olr1082 query olfactory receptor gene
PATHWAY

10. PATH:rno04740
odorant( )
↓
Golf (G protein)
↓
AC (adenylate cyclase)
↓
cAMP
↓
CNG (cyclic nucleofde gated channel)
↓
Ca2+
↓
CLCA (chloride channel calcium acfvated)

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. 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. 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. Togo WS SOAP
TogoWS SOAP
CLUSTALW
BLAST CLUSTALW SOAP

15. TogoWS SOAP
Ruby, Perl Python, Java 4
Ruby

16. ( )
hNp://togodb.dbcls.jp/ws_service

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. 1) REST
2) query (BLAST)
3)
4) CLUSTALW alignment
CLUSTALW
BLAST
sequencer alignment
CLUSTALW alignment (mulfple alignment)
matrix alignment

19. SOAP
[database ]
CotEditor Macintosh HD/ /tg03/bin
$cd bin
$ruby [ .rb]

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. 2) Sonic Hedgehog query
BLAST
DdbjBlastSearchSimple.rb (SOAP )
[SHH ]
#
blast_shh

22. BLAST
E‐value
alignment
Swissprot ID

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.
REST
hNp://togows.dbcls.jp/entry/ebi‐uniprot/Q62226.fasta

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. 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. CLUSTALW
alignment
Courier

28. Makorin1 mulfple alignment
1) REST Makorin1
2) query BLAST
3) BLAST
4) BLAST 8 CLUSTALW alignment

29. KEGG
TogoWS SOAP
TogoWS REST SOAP