Changes between Version 17 and Version 18 of DDBJ-KEGG-PDBj

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Timestamp:
2009/03/19 10:05:30 (15 years ago)
Author:
akinjo
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  • DDBJ-KEGG-PDBj

    v17 v18  
    3131 1. Group the blast results according to biological species (s''1'', s''2'', ..., s''n''). 
    3232 1. For each pathway component (c''i''), pick the top hit from each species. 
    33   *  At this step, you have (at most) an ''m'' compoents X ''n'' species array of protein sequences: '''Homologous Compoenents Matrix''' (HCM). 
     33  *  At this step, you have (at most) an ''m'' compoents X ''n'' species array of protein sequences: '''Homologous Compoenents Matrix''' (HCM) or more commonly called ''Phylogenetic profile''. 
     34 
    3435=== Part III === 
    3536Using Sequence Navigator API (PDBj): http://pdbjs3.protein.osaka-u.ac.jp/seqnavix/soap/index.html 
     
    7172 
    7273== For each species, select the top hit for each pathway component == 
    73 That is, filling the Homologous Components Matrix. 
     74That is, filling the phylogenetic profile. 
    7475In doing so, just select the top hit for each component for each species. 
    7576{{{ 
     
    102103 * Sometimes, two or more genes may be merged in one sequence. In that case, they will match the same chain ID but with non-overlapping regions. 
    103104 
     105= [[Timestamp]] = 
     106 * Part I is done. Part II is almost done. working on the routine for filling phylogenetic profile. 
     107 * Ogishima-san says he can draw the colored pictures of the final output. 
    104108 
    105109