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HOSEpipe--a WWW-hosted data management and analysis system for STS content mapping projects

M A Strivens1, P Middlehurst, S D Brown

  • 1MRC Mouse Genome Centre and MRC Mammalian Genetics Unit, Harwell, OX11 ORD, UK.

Mammalian Genome : Official Journal of the International Mammalian Genome Society
|July 1, 1997
PubMed
Summary

HOSEpipe is a new data management system for STS content mapping projects. It aids sample tracking and data analysis, supporting physical mapping and other genomics research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • STS content mapping projects require robust data management for sample tracking and analysis.
  • Existing systems may not adequately support the complexities of large-scale physical mapping.

Purpose of the Study:

  • To develop and present the HOSEpipe (High Output STS Evaluation pipeline) system.
  • To provide a WWW-based solution for managing data in STS content mapping.
  • To support whole chromosomal physical mapping projects.

Main Methods:

  • Development of a World Wide Web (WWW) server-based data management system.
  • Implementation of two core modules: sequence evaluation/annotation and YAC library STS screening.
  • Integration of sample processing, data entry, and experimental data analysis functionalities.

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Main Results:

  • HOSEpipe facilitates de novo sequence evaluation, STS screening against databases, and primer design.
  • The system enables efficient YAC library STS screening with integrated sample tracking and data analysis.
  • Successful application of HOSEpipe in a whole chromosomal physical mapping project.

Conclusions:

  • The HOSEpipe system effectively manages data for STS content mapping and physical mapping projects.
  • Its modular design and WWW accessibility make it adaptable for various project sizes and resolutions.
  • The approach is applicable to diverse genomics research, including sample sequencing and sequence-ready map construction.