Version 13 (modified by akinjo, 6 years ago)

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Description of services

  • DDBJ
  • PDBj
  • KEGG
  • CBRC

DDBJ

 http://www.xml.nig.ac.jp/index.html

  • data retrieve
  • sequence search and analysis
  • derived DBs
  • other DBs

PDBj

KEGG

 http://www.genome.jp/kegg/soap/doc/keggapi_manual.html

first concentrate on sequence + alignment

functional annotations

a given structure with unknown function -> BLAST at DDBJ / KEGG -> no homologs then -> struct-navi

  • accession number -> fasta
  • PDB ID <-> KEGG GENES ID get_linkdb_between_databases(string:from_db, string:to_db, int:offset, int:limit)
  • PDB ID <-> DDDBJ ID

proposed workflow(s)

functional (or structural) annotation of a protein sequence.

let hits = BLAST_DDBJ(fasta) if func_known(hits) then

return hits

else

let new_hits = BLAST_PDBj(fasta)

if exists(new_hits) then

foreach hit in new_hits do

let shits = struct_navi(hit)

if exists(shits) then

return shits

done

SOAP vs. REST

  • SOAP isn't good at huge data (big XML file)?
  • REST requires more coding on the client side. User must handle output data (XML or flat text...)
  • REST cannot do complicated stuffs?
  • No language supports the full SOAP spec.
  • Only a few languages have SOAP libraries.

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