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Related Experiment Videos

FOUNTAIN: a JAVA open-source package to assist large sequencing projects.

J M Buerstedde1, F Prill

  • 1Department of Cellular Immunology, Heinrich-Pette-Institute, Martinistr 52, 20251 Hamburg, Germany. buersted@genetics.hpi.uni-hamburg.de

BMC Bioinformatics
|October 10, 2001
PubMed
Summary
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FOUNTAIN is a new, open-source software package designed to manage large DNA sequencing projects. It simplifies data generation, storage, and analysis for smaller labs, facilitating comparative genomics research.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Increased DNA sequencing activities due to automation and lower costs.
  • Challenges in data management for smaller laboratories undertaking sequencing projects.
  • Need for efficient documentation, storage, annotation, and analysis of sequencing data.

Purpose of the Study:

  • To introduce FOUNTAIN, a software program for managing large DNA sequencing projects.
  • To address the data processing and storage difficulties faced by smaller research laboratories.
  • To provide a flexible and scalable solution for sequencing project management.

Main Methods:

  • Development of FOUNTAIN using JAVA and a relational database.
  • Web browser interface for user input and data management.

Related Experiment Videos

  • Integration of BLAST searches for sequence annotation against public databases.
  • Implementation of algorithms for sequence clustering and polymorphism detection.

    • Main Results:

    • FOUNTAIN facilitates the management of sequencing objects (clones) through various project stages.
    • Generated sequences are imported and annotated using BLAST.
    • The software includes tools for sequence clustering and identifying potential polymorphic positions.
    • FOUNTAIN provides a user-friendly web interface for data input and management.

    Conclusions:

    • FOUNTAIN is a simple, flexible, and scalable software package for large sequencing projects.
    • The open-source nature and database independence promote community improvement and extension.
    • The software aids in data generation and storage, supporting comparative genomics.