Changes between Version 16 and Version 17 of DDBJ-KEGG-PDBj

Timestamp:

2009/03/18 11:24:34 (16 years ago)

Author:

akinjo

Comment:

--

DDBJ-KEGG-PDBj

@@ -20 +20 @@
 
 === Part I ===
+Using KEGG API: http://www.genome.jp/kegg/soap/
+
  1. Pick a pathway of a specific organism, say Glycolysis / Gluconeogenesis pathway of Homo sapiens (human).
  1. Get all the amino acid sequences of that pathway component (c''1'', c''2'', ..., c''m'').
 
 === Part II ===
+Using WABI (DDBJ): http://xml.nig.ac.jp/index.html
+
  1. Run blast for each sequence against !UniProt(!SwissProt / TrEMBL).
  1. Group the blast results according to biological species (s''1'', s''2'', ..., s''n'').
@@ -29 +33 @@
   *  At this step, you have (at most) an ''m'' compoents X ''n'' species array of protein sequences: '''Homologous Compoenents Matrix''' (HCM).
 === Part III ===
+Using Sequence Navigator API (PDBj): http://pdbjs3.protein.osaka-u.ac.jp/seqnavix/soap/index.html
+
  1. Pick one column (species) of the HCM (s''j'') For each component of that column, run blast against PDB sequences.
   * You will have a list of PDBID and Chain ID as a result of this blast search.
@@ -97 +103 @@
 
 
+
+