Changes between Version 2 and Version 3 of DDBJ-KEGG-PDBj/Draft

Show
Ignore:
Timestamp:
2009/06/29 15:52:09 (12 years ago)
Author:
akinjo
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • DDBJ-KEGG-PDBj/Draft

    v2 v3  
    44 
    55= A DDBJ-KEGG-PDBj workflow: from pathways to protein-protein interactions = 
    6 The objective of this working group is to examine the potentials and obstacles of web services by implementing a real-life use case. 
     6The objective of this satellite group is to examine the potentials and obstacles in web services by implementing a real-life use case. 
    77The goal of the workflow is to enumerate possible physical protein-protein interactions among proteins in a biochemical pathway. 
    88More specifically, the workflow proceeds as follows.  
    99(1) The user provide a KEGG pathway ID. 
    10 (2) Extract the amino acid sequence of each enzyme in the specified pathway. 
    11 (3) For each amino acid sequence, run BLAST search against Swiss-Prot database. 
     10(2) Extract the protein sequence of each enzyme in the specified pathway. 
     11(3) For each protein sequence, run BLAST search against Swiss-Prot database. 
    1212(4) Construct a phylogenetic profile (a species-by-enzyme matrix) by identifying the top hits for each proteins and each species. 
    13 (5) For each species in the phylogenetic profile, run BLAST searches for each amino acid sequence against PDB. 
    14 (6) If two amino acid sequences (of the same species) have homologs in the same PDB entry, they are inferred to be in possible contact, and hence predicted to be an interacting pair. 
     13(5) For each species in the phylogenetic profile, run BLAST searches for each protein sequence against PDB. 
     14(6) If two amino acid sequences (of the same species) have homologs in the same PDB entry, they are inferred to be in physical contact, and hence predicted to be an interacting pair. 
     15(7) Output image files highlighting the conserved and interacting proteins in the pathway map. 
    1516 
    16 To implement the workflow outlined above, we have used the SOAP and REST APIs of DDBJ (http://www.ddbj.nig.ac.jp/), KEGG (http://www.genome.jp/) and PDBj (http://www.pdbj.org/). 
     17To implement the workflow outlined above, we have used the SOAP and REST APIs of DDBJ (http://www.ddbj.nig.ac.jp/), KEGG (http://www.genome.jp/) and PDBj (http://www.pdbj.org/). The workflow can be divided into three parts corresponding to the three web sites. Part I consists of steps (1) and (2) (using KEGG API), Part II of steps (3) and (4) (using DDBJ WABI), Part III of steps (5) and (6) (using PDBj sequence navigator SOAP); step (7) is handled by a customized program on the client side.