Biofacet Engine 2

The Biofacet Engine is the BIOFACET core technology implementing large scale management, querying, and sequence comparison of sequence databases.
The Biofacet Engine core is a high-performance software, written in C/C++. It is composed of several layers, including but not limited to: a proprietary sequence database storage format, an Object-Oriented Storage Manager (based on open source EyeDB), a word-indexing and retrieval engine, a complete scripting language (aka BFQL) bind to low level data structures and indexes, and numerous sequence alignment algorithms (public domain and proprietary).

It is a constantly evolving product supporting BiofacetCast and allowing real-time answers from BiofacetWeb and BiofacetSNP front-ends.

Biofacet Engine 2 is a major evolution of the genuine Biofacet Engine. Novelties include, but are not limited to:
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• Core:
  
  • Complete rewrap of core functions in C++, extension of storage model.
  • A new sequence database parser allowing storing and retrieving sequence databases in their original format and indexing of complete content.
    
  • Extended handling of metainfo information, improved implementation of collections.
    
    
• BFQL:
  • Redesign of the programming language.
  • Addition of many low-level APIs to the core engine, inclusion of standard and custom library functions, as well as fine-grained controls over indexing (link to BFQL API).
  • A new storage format for keywords indices, pushing limitations of number of objects and size up to operating system limit values.
  • Full interoperability with json data structures, almost used natively.
    
    
• New algorithms:
  • KERR-MULTIHITS
  • KMIRNA: microRNA identification specialized algorithm
    (patent pending EP3185157A1: Computer-implemented method for the identification of micrornas).
  • Improvements of read-mappers.
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• “BiofacetSNP Engine”: specific algorithmics and data-structure addition, dedicated to sequence variants management (see BiofacetSNP).