Question: Annotating yeast ORFs with GO and KEGG
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gravatar for Shih-Te Yang
15.9 years ago by
Shih-Te Yang80
Shih-Te Yang80 wrote:
Dear all: I am wondering to annotate each of Yeast genes or ORFs with GO and KEGG pathway. As you had known, the package of "AnnBuilder" and metadata of "GO"/"KEGG" can provide the functions about what are genes involved in the specific GO category and KEGG pathway. However, I am interested in what are the GO terms or KEGG belong to the genes I want!! Please see the format below: ORF GO KEGG YAL001C .. .. YAL002W .. .. YAL003W .. .. YAL004W .. .. .. .. .. How can I annotate these kind of information? Regards, Shih-Te ------------------------------------------------ Shih-Te Yang, Ph.D. student Bioinformatics Research Center Institute of Biochemistry School of Life Science National Yang-Ming University Tel:+886-2-28267000*5666 Fax:+886-2-81461062 E-mail:g38903040@ym.edu.tw MyWeb: http://binfo.ym.edu.tw/styang/
go yeast annotate category • 619 views
ADD COMMENTlink modified 15.9 years ago by Ken Simpson70 • written 15.9 years ago by Shih-Te Yang80
Answer: Annotating yeast ORFs with GO and KEGG
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gravatar for Ken Simpson
15.9 years ago by
Ken Simpson70
Ken Simpson70 wrote:
Hi Shih-Te, Use the lookUp function (devel version of the annotate package) or multiget (older version) to obtain the quantities of interest. e.g. > lookUp("YAL001C","YEAST","GO") <na> <na> <na> "GO:0000127" "GO:0003709" "GO:0006384" > multiget(c("YAL001C","YAL002W"),envir=YEASTGO) $YAL001C <na> <na> <na> "GO:0000127" "GO:0003709" "GO:0006384" $YAL002W <na> <na> <na> "GO:0045324" "GO:0005554" "GO:0005624" KEGG information is available for some organisms, but not (IIRC) yeast, yet. Do help(package=YEAST) to see the available annotation data. Cheers, Ken On Mon, 17 Nov 2003, Shih-Te Yang wrote: > Dear all: > > I am wondering to annotate each of Yeast genes or ORFs with GO and KEGG > pathway. As you had known, the package of "AnnBuilder" and metadata of > "GO"/"KEGG" can provide the functions about what are genes involved in the > specific GO category and KEGG pathway. > > However, I am interested in what are the GO terms or KEGG belong to the > genes I want!! Please see the format below: > > ORF GO KEGG > YAL001C .. .. > YAL002W .. .. > YAL003W .. .. > YAL004W .. .. > .. .. .. > > How can I annotate these kind of information? > > Regards, > Shih-Te
ADD COMMENTlink written 15.9 years ago by Ken Simpson70
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