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 (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:
- 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.
- 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.
- New algorithms:
- KMIRNA: microRNA identification specialized algorithm
(patent pending EP3185157A1: Computer-implemented method for the identification of micrornas).
- Improvements of read-mappers.
- “BiofacetSNP Engine”: specific algorithmics and data-structure addition, dedicated to sequence variants management (see BiofacetSNP).