Genomics
Description:Genomics encompasses the different aspects of the studies of nucleotides (DNA, RNA’s) which have been made possible thanks to the increasing use of breakthrough technologies such as micro-arrays/biochips, PCR (Polymerase Chain Reaction) and Next Generation Sequencing (NGS),...Micro-arrays:Micro-array has been and remains one of the cornerstone technologies used routinely and extensively within the Life Sciences R&D and Molecular Diagnostics activities to help scientists to gain minute and accurate understanding of life mechanisms (e.g. diseases etiology, cells, tissues and organs developments, drugs’ efficacy and safety,...). The intensive use of micro-arrays is strongly linked to the successful development of specific bioinformatics tools if only to deal with the amount of data generated and their proper analysis.In that field BioXpr is mainly acting on two levels: Firstly BioXpr has the relevant statistical knowledge to analyse and correlate the experimental results from the different types of commercialised micro-arrays ranging from low density /customized micro-arrays to high density micro-arrays (Affymetrix, Agilent,...)
CASE STUDY 1
Secondly and more upstream BioXpr has the expertise to design both the oligo probes to be spotted on low and medium density micro-arrays and the corresponding micro-arrays themselves.
CASE STUDY 2
PCR – Polymerase Chain Reaction:BioXpr’quantum chemists have always shown a keen interest in the better understanding of the thermodynamics underlying the PCR-based technology. Years of intensive research led to the design of optimized proprietary algorithms and formulae ensuring a more accurate and robust prediction of decisive parameters such as the melting temperature and delta G (lien vers sheet Tm). Concomitantly BioXpr developed a purpose-built software module library to· compute numerous properties of any type of nucleotide sequences such as DNA, RNA, PNA (Peptide Nucleic Acids) and also amino-acids· design primers for “Hot” and “Cold” PCR-based assays and related probes such as TaqMan, TaqMan MGB, Molecular Beacons, Scorpions, MLPA (Multiplex Ligation-dependent Probe Amplification,...· set up Multiplex PCR assays,· perform in-silico PCR to ensure of the quality and the specificity of the binding of the primers to the targeted sequence,.... See “Solutions” for more info...(lien vers “Solution for biochips and PCR-based Molecular Diagnostics”)
CASE STUDY 3Next Generation Sequencing:The R&D activities of Life Science companies are going through an exciting new phase of change andgrowth as a result of the opportunities offered by Next Generation Sequencing. These novel approaches are progressively delivering on their promise as to sequence DNA at an unprecedented speed and quality, enablingimpressive scientific achievements and novel applications. New Generation Sequencing has already demonstrated great impact on different areas of Life Science sectors such as in medical, microbial, animal and plant research. Additionally, Next Gen Sequencing has equally huge potential as a tool for drug discovery, transcriptomics for instance. The data processing workflow for Next Gen Sequencing can be described as follows: (to insert the slide on the workflow)Because of the ever increasing data ouput of these new sequencing technologies the researchers are faced with new challenges with respect to data management, analysis and interpretation in other words once the scientist get its sequencing results it is of paramount importance for him to further investigate information such as the corresponding genes and proteins encoded within the sequence of interest. Furthermore it might be equally important to be able to automatically characterize the sequence-encoded proteins such as physico-chemical properties, 2D and 3D structures, and the relevant signaling pathways (e.g.diseases patterns) these proteins are involved in. Even if BioXpr is perfectly capable of assemblying reads into contigs generated by either Illumina , Roche or ABi sequencers by using different commercially-available software such as Assembler our real added value lies within our capacity to automatically and fully annotate the sequences of interest.BioXpr is currently developing full annotation and visualization analysis pipe-line for both prokaryotic (e.g.bacteria) and eukaryotic (human, rat, mouse and plant) genomes. (Insert the slide about Bacterial Genome Annotation pipeline) See more info on “Solutions for Next Generation Sequencing and Genome Annotation”(insert the link)
BioXpr can also act more upstream in the sequencing process should Re-sequencing and / or Gap Closer be required. For Re-sequencing BioXpr can design primers allowing easy assembling of amplicons and test those for specifity against the whole genome or the set of contigs by either using the BioXpress (link to BioXpress) server software or by BLAST. Similarly for Gap Closure one can easily find appropriate primers to close the gaps whatever Template or De Novo sequencing and test those for specifity against the whole genome or the set of contigs by either using the BioXpress (link to BioXpress) server software or by BLAST.
