Open Source: Bioinformatics tools from Jena facilitate phage detection and PCR design
In two scientific publications, InfectoGnostics researchers recently presented new bioinformatics tools whose open source code can now be used and further developed for free. The “What the Phage” software enables the detection of phages, while the “ConsensusPrime” can be used for the development of various molecular tests. The tools have been developed by researchers from the University Hospital Jena (UKJ), Leibniz Institute for Photonic Technologies (Leibniz-IPHT) and startup nanozoo.
Bacteriophages, or phages for short, are viruses that infect bacteria and have therefore again come into focus for therapeutic applications in recent years. Especially for antibiotic-resistant pathogens, phage therapies may be a promising option. To date, however, phages and their influence on microbiomes in the environment and in humans have been little researched.
“Although there is more and more data from sequenced microorganisms, it has not yet been systematically investigated which phages occur. To solve this problem, we have developed What the Phage together with colleagues from nanozoo and Leibniz IPHT. The software provides a workflow that can use machine learning and other algorithms to detect phages and predict possible new variants from sequence data,” said Mike Marquet, UKJ researcher and lead author of the recent publication What the Phage in GigaScience.
With What the Phage, several programs were combined into one workflow and optimized for the fastest and simplest possible evaluation of the user. The researchers deliberately chose a modular open source principle, which Mike Marquet explains further: “We want the workflow to be continuously expanded and improved. For example, predictions for prophets are conceivable. Other developers have already contributed code and additional know-how to this.”
— ConsensusPrime simplifies primer design for new PCR tests —
PCR, the polymerase chain reaction, is considered the methodological gold standard for precise molecular laboratory testing in the field of infection science. Samples of genetic material characteristic of the pathogen being sought can be reproduced using the molecular biological method and thus detected.
But in order for the eponymous enzyme – DNA polymerase – to ‘know’ which parts of DNA it needs to duplicate, the researchers design so-called “primers” – short sections of DNA to which the polymerase binds. With ConsensusPrime, researchers from the department “Optical-Molecular Diagnostics and Systems Technology” at Leibniz-IPHT have developed a bioinformatics tool that enables faster and more efficient design of primers.
When designing primers, researchers often face the problem that they do not want to detect or distinguish just one pathogen strain, but rather several very closely related ones. At the same time, however, a primer must also be adapted as specifically as possible to the target genome. In such cases, one often looks for a so-called “consensus primer”: a sequence that has the greatest similarity to several strains, but is still ideally suited as a primer.
“Without our software, you usually have to manually select the sequence sections that show similarities. This is not only imprecise, but with large amounts of data it is hardly manageable and also very time-consuming. ConsensusPrime directly filters out unsuitable primers and precisely calculates the genome sections with the largest similarities. With our pipeline, we get a consensus sequence for the optimal primer,” explains Dr. Maximilian Collatz, Leibniz IPHT researcher and lead author of the publication in “Biomedinformatik”.
What subject | https://github.com/replication/What_the_Phage
Mike Marquet, Martin Hoelzer, Mathias W Pletz, Adrian Viehweger, Oliwia Makarewicz, Ralf Ehricht, Christian Brandt. 2022. What phage: a scalable workflow for the identification and analysis of phage sequences, GigaScience, Volume 11, giac110.
ConsensusPrime | https://github.com/mcollatz/ConsensusPrime
Maximilian Collatz, Sascha D. Braun, Stefan Monecke and Ralf Ehricht. 2022. “ConsensusPrime—A Bioinformatic Pipeline for Ideal Consensus Primer Design” BioMedInformatics 2, No. 4: 637-642.
Two new bioinformatics tools from Jena improve phage detection and primer design for PCR …
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