User:Vincent Rouilly/Part Registry DAS server: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
Line 43: Line 43:
** '''types''': [http://127.0.0.1/cgi-bin/das/miniregistry/types http://127.0.0.1/cgi-bin/das/miniregistry/types]
** '''types''': [http://127.0.0.1/cgi-bin/das/miniregistry/types http://127.0.0.1/cgi-bin/das/miniregistry/types]
* DNA reference server:
* DNA reference server:
** '''full BBa_B0015 DNA sequence''': [http://127.0.0.1/cgi-bin/das/miniregistry/dna?BBa_B0015 http://127.0.0.1/cgi-bin/das/miniregistry/dna?BBa_B0015]
** '''full BBa_B0015 DNA sequence''': [http://127.0.0.1/cgi-bin/das/miniregistry/dna?segment=BBa_B0015 http://127.0.0.1/cgi-bin/das/miniregistry/dna?BBa_B0015]
** '''BBa_B0015 DNA sequence from 30bp-110bp: [http://127.0.0.1/cgi-bin/das/miniregistry/dna?BBa_B0015=30,110 http://127.0.0.1/cgi-bin/das/miniregistry/dna?BBa_B0015=30,110]
** '''BBa_B0015 DNA sequence from [100bp-110bp]: [http://127.0.0.1/cgi-bin/das/miniregistry/dna?segment=BBa_B0015:100,110 http://127.0.0.1/cgi-bin/das/miniregistry/dna?segment=BBa_B0015:100,110]
* Assembly info:
* Assembly info:
** '''sub-components''': [http://127.0.0.1/cgi-bin/das/miniregistry/features?segment=BBA_B0015;category=structural http://127.0.0.1/cgi-bin/das/miniregistry/features?segment=BBA_B0015;category=structural]
** '''sub-components''': [http://127.0.0.1/cgi-bin/das/miniregistry/features?segment=BBA_B0015;category=structural http://127.0.0.1/cgi-bin/das/miniregistry/features?segment=BBA_B0015;category=structural]

Revision as of 07:03, 21 July 2009

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)

Retrieved from "https://openwetware.org/mediawiki/index.php?title=User:Vincent_Rouilly/Part_Registry_DAS_server&oldid=326401"