Turna, J. | Search bioRxiv

bioRxiv2020

PHERI - Phage Host Exploration tool.

Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multi-resistant bacterial strains occurring in all world regions. One of the possible future solutions is the use of bacteriophages in therapy. Bacteriophages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm based tool called PHERI. PHERI predicts suitable bacterial host genus for purification of individual viruses from different samples. Besides, it can identify and highlight protein sequences that are important for host selection. PHERI is available at https://hub.docker.com/repository/docker/andynet/pheri. The source code for the model training is available at https://github.com/andynet/pheri_preprocessing, and the source code for the tool is available at https://github.com/andynet/pheri.

bioinformatics↗

bioRxiv2018

Innovative method for reducing uninformative calls in non-invasive prenatal testing

MotivationNon-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test.\n\nResultsWe propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls.\n\nAvailability and ImplementationA particular implementation of the proposed methods is not provided with the manuscript.\n\nContactCorrespondence regarding the manuscript should be directed at Frantisek Duris (fduris@dcs.fmph.uniba.sk).\n\nSupplementary InformationNo additional supplementary information is available.

bioinformatics↗