User:Vincent Rouilly/Part Registry DAS server

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Distributed Annotation System (DAS) resources

  • biodas.org website
  • Current specifications (v1.53)
  • DAS compliant software tools:
    • Servers:
      • LDAS (Light DAS)
      • ...
    • Clients:
    • Web services:
      • ...

Building a local Part Registry DAS server

Prerequisites

  • Software installations:
    • BioPython
    • local Blast
    • BioPerl
    • MySQL database + BioSQL SQL script
    • Apache server
    • LDAS server
  • latest FASTA dump from Part Registry

Step 1

  • BioPython processing
    • Load FASTA part file
    • Clean-up FASTA part file by removing all parts with no sequences (Blast doesn't handle them)
    • For each part:
      • Blast part against the rest of the parts, looking for perfect match.
      • Annotate part with perfect matches in order to store assembly information
      • Store part in BioSQL database

Step 2: generate LDAS files

  • ...

Step 3: configure and test DAS server

  • ...

Local server (personal use only)