Bioinformatics tools for phage detection and PCR design

Bacteriophages, or phages for short, attack bacteria and have therefore once again become the focus of attention for therapeutic applications in recent years. Phage therapies could be a promising option, especially for antibiotic-resistant pathogens. To date, however, phages and their influence on microbiomes in the environment and in humans have been little researched.

„Although more and more data is available from sequenced microorganisms, there has been no systematic investigation into which phages occur. To solve this problem, we have developed What the Phage together with colleagues from Nanozoo and the Leibniz IPHT. The software provides a workflow that uses machine learning and other algorithms to detect phages and predict possible new variants from sequence data“, explains Mike Marquet, UKJ researcher and lead author of the recent publication on „What the Phage“ in „GigaScience“.

In „What the Phage“, several programs were combined into one workflow and optimised for the quickest and easiest possible evaluation by the user. The researchers deliberately opted for a modular open source principle, as Mike Marquet explains: „We want the workflow to be continuously expanded and improved. For example, predictions for prophages are conceivable. Other developers have already contributed code and further expertise.β

Software „ConsensusPrime“

PCR, polymerase chain reaction, is regarded as the methodological gold standard for precise molecular laboratory tests in infectiology. Sections of genetic material that are characteristic of the pathogen in question can be amplified and thus detected using this molecular biological method. However, to ensure that the enzyme that gives the method its name - DNA polymerase - knows which DNA segments it needs to replicate, scientists design so-called primers to which the polymerase binds. With ConsensusPrime, scientists from the Department of Optical-Molecular Diagnostics and Systems Technology at Leibniz IPHT have developed a bioinformatics tool that makes it possible to design primers more quickly and efficiently.

When designing primers, researchers are often faced with the problem of having to detect or differentiate not just one but several very closely related pathogen strains. At the same time, a primer must also be as specific as possible to the target genome. In such cases, a so-called „consensus primer“ is often sought: a sequence that has the greatest „similarity to several strains, but is nevertheless optimally suited as a primer.

„Without our software, you usually have to search for 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 filters out unsuitable primers directly and calculates exactly the genetic segments with the greatest similarities. With our pipeline, we thus obtain a consensus sequence for the optimal primer“, explains Dr Maximilian Collatz, Leibniz IPHT researcher and lead author of the publication in „Biomedinformatics“.

Software and publications:

What the Phage | https://github.com/replikation/What_the_Phage
Mike Marquet, Martin Hölzer, Mathias W Pletz, Adrian Viehweger, Oliwia Makarewicz, Ralf Ehricht, Christian Brandt. 2022. What the Phage: a scalable workflow for the identification and analysis of phage sequences, GigaScience, Volume 11, giac110. DOI: 10.1093/gigascience/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. DOI: 10.3390/biomedinformatics2040041

Article from "LABO" dated 27 February 2023