ERCIM News No.37 - April 1999
Gene-IT - A new INRIA Spin-off Company
by Jean-Jacques Codani
Gene-IT SA is a new start up of INRIA, active in the BioInformatics sector. Gene-ITs core technology is based on LASSAP (LArge Scale Sequence compArison Package), a multiple algorithms, intra- and inter- databases high performance search engine, running on Unix platforms. It is a modern open system, based on a new approach to sequence comparison (genomic, proteic, EXTs, patterns,...). LASSAP provides biologists tools and methods that rigorously test their understanding of Genomics.
Designed to fit the needs of large-scale sequence analysis, LASSAP has unique capabilities to analyse very large data sets of sequence and pattern. By handling annotation and sequence information simultaneously, LASSAP allows the scientist to ask complex queries on databases or clusters of databases.
Various post-analysis techniques can be performed on the results, from simple selections on alignment properties up to clustering analysis, allowing complex line of thought theories to be tested and answered immediately. The versatility of LASSAP allows different tasks to be performed by the scientist from a simple web based client environment, for example:
- improvements of sequence quality and automatic analysis within sequencing centres
- complex scanning on nucleic, proteic, ESTs and motifs databases
- building protein families
- reducing database redundancy, checking for patents by using proprietary algorithms.
From an application point of view, LASSAP allows to build or to find families of proteins, among entire genomes and/or specific sets. This process relies on an in-depth study of gene duplications, which lead to the disclosure of a number of unexpected and singular regularities, which have a strong predictive value and can be viewed therefore as laws of Genomics.
As a consequence, this straightforward and rigorous methodology is a powerful automatic annotation tool, which favourably impacts on any Drug Discovery process. Moreover, once a family of protein has been chosen, LASSAP can perform complex tasks, mixing public domain and private databases (such as Geneseq and LifeSeq) to reduce the set of ESTs candidates, relative to this family. This methodology reduces drastically the amount of work usually needed to select EST clones as a genetic material for candidates.
LASSAP is progressive software, which does not pretend to provide the unique solution to the complex process of Drug Discovery. It has been devised to let scientist's design new strategies. They benefit from using a tool which lets them think in terms of science, and not in terms of informatics. LASSAP is not a fat genomic data management system designed to simplify navigation through mouse clicks, nor a single-use database: it is an automatic annotation tool, a data mining engine which provides new understanding and novel candidates.
Through its command line interface, LASSAP can be used by the BioInformatics team to implement sophisticated tasks. A Java front and back end is available which allows scientists to use the same functionality's using a Graphical User Interface. Its client/server model allows rapid deployment with minimum training to both BioInformatics and scientific personnel via the Intranet.
For more information, see: http://www.gene-it.com/
Jean-Jacques Codani - Gene-IT S.A.
Tel: +33 1 39 63 52 48