Publications by authors named "Jan Badura"
Article Synopsis
- RNA molecules are crucial for various biological processes like gene regulation and protein synthesis, and their specific structures are key to their functionality, which makes them useful in bioengineering therapeutics.
- Recent advancements in computational tools have enhanced the ability to predict RNA sequences with specific folding properties, but there is still a need for standardized datasets to evaluate these tools.
- This study introduces a comprehensive dataset of internal and multibranched loops from RNA structures, alongside benchmarking tests of popular RNA design algorithms using this dataset.
Motivation: There are very few methods for de novo genome assembly based on the overlap graph approach. It is considered as giving more exact results than the so-called de Bruijn graph approach but in much greater time and of much higher memory usage. It is not uncommon that assembly methods involving the overlap graph model are not able to successfully compute greater datasets, mainly due to memory limitation of a computer.
View Article and Find Full Text PDFNext generation sequencers produce billions of short DNA sequences in a massively parallel manner, which causes a great computational challenge in accurately reconstructing a genome sequence de novo using these short sequences. Here, we propose the GRASShopPER assembler, which follows an approach of overlap-layout-consensus. It uses an efficient GPU implementation for the sequence alignment during the graph construction stage and a greedy hyper-heuristic algorithm at the fork detection stage.
View Article and Find Full Text PDF