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  1. Jalview
  2. JAL-1979

SIFTS End-To-End scanning

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    • Type: Task
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
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      Description

      The aim of this task is as follows:
         - To programmatically detect further unknown discrepancies with SIFTs data
         - To ensure that most SIFTS file is processed in a verifiable manner

      Jim suggested the following method:
         For each SIFTs record:
            * retrieve all UniProt sequences mapping to the record
                  jim to provide code to access a local copy of UniProt
                  output a fasta alignment for each distinct PDB chain/UniProt mapping: i.e.
                  >uniprot|<UniProt ID>/1-end
                  ASDASDASDASD
                  >pdb|<PDB ID+chainCode>/1-end
                  --DAS--ASD--ASD
            * compare all FASTA files with output produced by Fabio‚Äôs SIFTs/UniProt mapping script
            * if there are differences - find out why and fix !

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              Assignee:
              tcnofoegbu Tochukwu Charles N Ofoegbu
              Reporter:
              tcnofoegbu Tochukwu Charles N Ofoegbu
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                Updated: