KAAS annotate genes

  • Map gene sequences or protein sequences to kegg orthologs using kaas

KEGG ID trnasfer

  • ToGoWs: various types of KEGG IDs to NCBI and UniProt IDs.
    $ curl -s http://togows.dbcls.jp/entry/orthology/K08452,K13751/name
    SLC24A3, NCKX3
    $ for i in `cat ko.list`; do echo $i, \
    `curl -s http://togows.dbcls.jp/entry/orthology/$i/name`; done \
  • Bioconductor packages ``` library(org.Hs.eg.db)

##Toy example symbols: sym = c(“AKT3”,”CDH1”)

##Get the Entrez gene IDs associated with those symbols EG_IDs = mget(sym, revmap(org.Hs.egSYMBOL),ifnotfound=NA)

##Then get the KEGG IDs associated with those entrez genes. KEGG_IDs = mget(as.character(EG_IDs), org.Hs.egPATH,ifnotfound=NA) ```