Agmata, A. | bioRxiv Science

bioRxiv2024

ThermoPlex: An Automated Design Tool for Target-specific Multiplex PCR Primers based on DNA Thermodynamics

Multiplex PCR-based assays are indispensable platforms for rapid and cost-effective DNA-based multi-target detection. The success of such an assay highly depends on the accurate design of oligonucleotide primers, arguably its most vital component. In this study, the ThermoPlex design tool is introduced, offering an automated design pipeline for target-specific multiplex PCR primers motivated by DNA thermodynamics. From a sequence alignment of all relevant target and non-target sequences, ThermoPlex automatically designs multiplex PCR primer candidates in just a matter of minutes. The software also offers tools for thermodynamic calculations that can either be used apart from the automated primer screening routine or in conjunction with other existing primer design tools, depending on the on the needs of the user. Evidences presented here in this study provide insights on the performance of the software through theoretical and experimental analyses, serving to establish the reliability of its framework.

bioinformatics↗

bioRxiv2024

Convolutional-LSTM Approach for Temporal Catch Hotspots (CATCH): An AI-Driven Model for Spatiotemporal Forecasting of Fisheries Catch Probability Densities

Efficient fisheries management is crucial for sustaining both marine ecosystems and the economies that heavily depend on them, such as Iceland. Current fishing practices involve decisions informed by a combination of personal experience, current data on environmental and oceanographic conditions, reports from other captains, and target species within the constraints of the fishing quota. However, the intricate spatiotemporal dynamics of fish behaviour make it difficult to predict fish stock distributions. Despite technological breakthroughs in fishing vessel data collection, much of the decision-making still relies heavily on subjective judgment, highlighting the need for more robust, data-driven predictive methods. This paper presents CATCH, a convolutional long short-term memory neural network model that forecasts fish stock probability densities over time and space in Icelandic waters. The framework represents the first utilization of large-scale Icelandic fishing fleet data integrating multidimensional inputs like depth, bottom temperature, and catch data to produce accurate, multivariate forecasts. The model demonstrates high accuracy, low error metrics, and strong structural similarity to observed data, generalizing well across key species such as Atlantic cod, haddock, saithe, golden redfish, and Greenland halibut. Its promising results suggest deep learning models have the potential to optimize fisheries operations, enhance sustainability, and support data-driven decision-making.

bioinformatics↗