Biology subjects

Eulenfeld, T.

Publications and source records attributed to Eulenfeld, T..

3 recordsLinked to original sources

bioRxiv2026

AssayBLAST v2: Major update improving reliability and reporting of the in silico analysis of molecular multi-parameter assays

IntroductionAccurate in silico evaluation of primers and probes is essential for the rational design of molecular multi-parameter assays. We present Assay-BLAST v2 to automate and simplify this process for extensive assay designs. ResultsA newly integrated strand and proximity check enables precise validation of corresponding oligonucleotides, ensuring correct orientation and spacing for efficient amplification. Based on predicted oligonucleotide interactions, Assay-BLAST v2 estimates amplification outcomes, offering a computational benchmark for downstream wet-lab validation and performance correlation. Additionally, the updated software integrates an adaptive BLAST parameter optimization that dynamically scales with database size, thereby improving both analytical sensitivity and computational performance. These improvements are supported by a comparative evaluation against the previous version of AssayBLAST. ConclusionsCollectively, these enhancements streamline the assay development workflow, reduce costs associated with suboptimal primer and probe synthesis, and increase the robustness and reliability of molecular diagnostics and research applications.

bioinformatics↗

bioRxiv2025

First full-genome alignment representative for the genus Pestivirus

The members of the genus Pestivirus in the family Flaviviridae comprise economically important pathogens of life stock like classical swine fever (CSFV) and bovine viral diarrhea virus (BVDV). Intense research over the last years revealed that at least 11 recognized and eight proposed pestivirus species exist. The single-stranded, positive-sense RNA genome encodes for one large polyprotein which is processed by viral and cell-derived proteases into 12 mature proteins. Besides its protein-coding function, the RNA genome also contains RNA secondary structures with critical importance for various stages of the viral life cycle. Some of those RNA secondary structures, like the internal ribosome entry site (IRES) and a 3 stem-loop essential for genome replication, had already been studied for a few individual pestiviruses. In this study, we provide the first genome-wide multiple sequence alignment (MSA) including all known pestivirus species (accepted and tentative). Moreover, we performed a comprehensive analysis of RNA secondary structures phylogenetically conserved across the complete genus. While showing well-described structures, like a 5 stem-loop structure, the IRES element, and the 3 stem loop SL I to be conserved between all pestiviruses, other RNA secondary structures in the 3 untranslated region (UTR) were only conserved in subsets of the species. We identified 29 novel phylogenetically conserved RNA secondary structures in the protein-coding region, with so far unresolved functional importance. The microRNA binding site for miR-17 was previously known in species A, B, and C; in this study, we identified it in ten additional species, but not in species K, S, Q, and R. Another interesting finding is the identification of a putative long-distance RNA interaction between the IRES and the 3 end of the genome. These results together with the now available comprehensive multiple sequence alignment including all 19 pestivirus species, represent a valuable resource for future research and diagnostic purposes.

bioinformatics↗

bioRxiv2025

AnchoRNA: Full virus genome alignments through conserved anchor regions

Multiple sequence alignment of full viral genomes can be challenging due to factors such as long sequences, large insertions/deletions (spanning several 100 nucleotides), large number of sequences, sequence divergence, and high computational complexity in particular when computing alignments based on RNA secondary structures. Standard alignment methods often face these issues, in particular when processing highly variable sequences or when specific phylogenetic analysis is required on selected subsequences. We present an algorithm to determine high quality anchors that define partitions of sequences and guide the alignment of viral genomes to respect well conserved, and therefore functionally significant, regions. This new approach is implemented in the Python-based command line tool AnchoRNA, which is designed to identify conserved regions, or anchors, within coding sequences. By default, anchors are searched in translated coding sequences accounting for high mutation rates in viral genomes. AnchoRNA enhances the accuracy and efficiency of full-genome alignment by focusing on these crucial conserved regions. AnchoRNA guided alignments are systematically compared to the results of 3 alignment programs. Utilizing a dataset of 55 representative Pestivirus genomes, AnchoRNA identified 55 anchors that are used for guiding the alignment process. The incorporation of these anchors led to improvements across tested alignment tools, highlighting the effectiveness of AnchoRNA in enhancing alignment quality, especially in viral genomes.

bioinformatics↗