Changes between Version 7 and Version 8 of DDBJ-KEGG-PDBj

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Timestamp:
2009/03/17 17:50:34 (15 years ago)
Author:
akinjo
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  • DDBJ-KEGG-PDBj

    v7 v8  
    3030== Here's a pathway of human == 
    3131[[Image(hsa00010.gif)]] 
     32== Pick amino acid sequences for the pathway components == 
     33{{{ 
     34>comp1 
     35..... 
     36>comp2 
     37.... 
     38>comp3 
     39.... 
     40}}} 
    3241 
    3342== After running blast for each pathway component == 
    3443You will have a list of proteins annotated with species. 
    3544{{{ 
    36 protein1 species1 evalue... 
    37 protein2 species2 evalue... 
    38 protein3 species1 evalue... 
    39 protein4 species2 evalue... 
    40 protein5 species3 evalue... 
     45Comp1 
     46  protein1 species1 evalue... 
     47  protein2 species2 evalue... 
     48  protein3 species1 evalue... 
     49  protein4 species2 evalue... 
     50  protein5 species3 evalue... 
     51... 
     52Comp2 
     53  protein1 species1 evalue... 
    4154... 
    4255}}} 
    4356 
    44 == Group blast hits by species == 
     57== For each species, select the top hit for each pathway component == 
     58That is, filling the Homologous Components Matrix. 
     59In doing so, just select the top hit for each component for each species. 
    4560{{{ 
    46 species1 
    47   protein1 
    48   protein3 
     61                 species1     species2   species3 ... 
     62------+--------------------------- 
     63comp1  | protein11   protein12 ... 
     64comp2  | protein21   protein22   protein23 ... 
     65comp3  | ... 
     66comp4  | ... 
     67.... 
     68}}} 
    4969 
    50 species2 
    51   protein2 
    52   protein4 
    53  
    54 species3 
    55   protein5 
    56  
    57 ...