BaseClear’s variant detection pipeline renewed
Variant detection is an important application of next-generation sequencing experiments. It involves the alignment of sequence reads to a reference and the detection of mutations …
Read moreThe rapid advancement in the genomics field opened new possibilities in biomarker and vaccine development. The availability of genomic data of pathogens increases the opportunities for the identification of novel vaccine candidates and allows one to move from a conventional empiric approach to a more rational design. This is also true for biomarker development and drug discovery related to infectious diseases. Various approaches are available to support in your research and development of biomarkers and vaccines for infectious diseases.
In order to identify a possible target for a biomarker or vaccine, it is necessary to compare the genomes of different pathogen variants and determine which genes they have in common and which genes are unique. To truly understand the behaviour of a certain pathogen, one must obtain not only information about its genome, but also about the gene expression under the given circumstances. Such information can be obtained via transcriptome analysis. A combination of both the sequencing of the transcriptome (mRNA) data a complete can be obtained to determine the gene expression and discover novel exons and alternative splicing.
Antibiotic resistance is a serious problem in the fight against infectious diseases. In case of an outbreak of a certain disease, it is necessary to check the antibiotic resistance of the pathogen that is causing the epidemic. However, screening pathogens for antibiotic resistance can be very laborious and time consuming. A new type of antibiotic resistance gene screening based on genomics is much more efficient than the classical screening methods. Using a new bioinformatics tool (developed by the BaseClear bioinformatics team), you can determine which antibiotic resistance genes are present in the genome of your microorganism. This genomics screening method can dramatically reduce the number of disk diffusion tests required. In the end, they might even replace them completely.
Virulence factors are molecules produced by pathogens that increase their effectiveness and help them to colonize and grow within a patient and circumvent and suppress the patient’s immune response. Knowledge about these virulence factors is essential for the development of biomarkers and vaccines. The virulence genes that are present in a certain pathogen can be identified and characterized by comparing its genome with the virulence genes that are described in a special, curated database.
High-quality synthetic DNA libraries can be used as an in vitro molecular evolution strategy. This is the most efficient way to create proteins and regulatory sequences with improved or even novel properties. A library might help improve the half-life of the biomarker or increase its binding affinities to receptors or ligands. We have extensive experience with a wide variety of libraries and can also produce libraries of large constructs. We can produce libraries with one or more specified mutations or combinations of these. We have fully automated systems for isolation and quantification of DNA, for colony picking and for screening of the libraries. As a result, we can do library projects with very short turnaround times.
Variant detection is an important application of next-generation sequencing experiments. It involves the alignment of sequence reads to a reference and the detection of mutations …
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While the European (EFSA) and American (FDA) regulatory bodies have established guidelines for the approval of novel microbial strains in food and feed applications, these …
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Obtaining regulatory approval to use microorganisms as food additive or production strain can be challenging. Applying the regulatory guidelines and rules to the genomic data …
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