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-IT’s 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/
Please contact:
Jean-Jacques Codani - Gene-IT S.A.
Tel: +33 1 39 63 52 48
E-Mail: gene-it@inria.fr
