Pegasys: Software for executing and integrating analyses of biological sequences

Sohrab P. Shah, David Y.M. He, Jessica N. Sawkins, Jeffrey C. Druce, Gerald Quon, Drew Lett, Grace X.Y. Zheng, Tao Xu, B. F. Francis Ouellette

Research output: Chapter in Book/Report/Conference proceedingChapter


Background We present Pegasys-a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. Results The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. Conclusions The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at

Original languageEnglish (US)
Title of host publicationData Structure and Software Engineering
Subtitle of host publicationChallenges and Improvements
PublisherApple Academic Press
Number of pages25
ISBN (Electronic)9781466562608
ISBN (Print)9781926692975
StatePublished - Apr 19 2016

ASJC Scopus subject areas

  • Computer Science(all)
  • Mathematics(all)


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