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

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Timestamp:
2009/03/18 11:24:34 (15 years ago)
Author:
akinjo
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  • DDBJ-KEGG-PDBj

    v16 v17  
    2020 
    2121=== Part I === 
     22Using KEGG API: http://www.genome.jp/kegg/soap/ 
     23 
    2224 1. Pick a pathway of a specific organism, say Glycolysis / Gluconeogenesis pathway of Homo sapiens (human). 
    2325 1. Get all the amino acid sequences of that pathway component (c''1'', c''2'', ..., c''m''). 
    2426 
    2527=== Part II === 
     28Using WABI (DDBJ): http://xml.nig.ac.jp/index.html 
     29 
    2630 1. Run blast for each sequence against !UniProt(!SwissProt / TrEMBL). 
    2731 1. Group the blast results according to biological species (s''1'', s''2'', ..., s''n''). 
     
    2933  *  At this step, you have (at most) an ''m'' compoents X ''n'' species array of protein sequences: '''Homologous Compoenents Matrix''' (HCM). 
    3034=== Part III === 
     35Using Sequence Navigator API (PDBj): http://pdbjs3.protein.osaka-u.ac.jp/seqnavix/soap/index.html 
     36 
    3137 1. Pick one column (species) of the HCM (s''j'') For each component of that column, run blast against PDB sequences. 
    3238  * You will have a list of PDBID and Chain ID as a result of this blast search. 
     
    97103 
    98104 
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