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Pegasys: software for executing and integrating analyses of biological sequences.
Sohrab P Shah1, David Y M He, Jessica N Sawkins
1UBC Bioinformatics Centre, University of British Columbia, Vancouver, British Columbia, Canada. sohrab@bioinformatics.ubc.ca
BMC Bioinformatics
|April 21, 2004
Summary
Pegasys is a flexible software system for biological sequence analysis. It enables users to create and manage custom analysis workflows, integrating data from diverse tools for efficient genomic research.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Biological sequence analysis involves integrating data from heterogeneous tools.
- Existing systems may lack flexibility and customization for complex workflows.
Purpose of the Study:
- To present Pegasys, a flexible, modular, and customizable software system.
- To facilitate the execution and data integration of diverse biological sequence analysis tools.
Main Methods:
- Development of a novel data structure for creating sequence analysis workflows.
- Implementation of a unified data model for storing analysis results.
- Dynamic workflow creation via a graphical user interface with parallel execution on compute clusters.
Main Results:
- Pegasys includes tools for sequence alignment, gene prediction, RNA detection, and repetitive sequence masking.
- Integrated results can be exported to General Feature Format (GFF) or GAME XML.
- The system supports programmatic data access via SQL queries.
Conclusions:
- Pegasys empowers biologists and bioinformaticians to build and manage sequence analysis workflows.
- The software is open-source (GNU GPL) and available for download with full documentation.