Christiansen Wiberg (nutoutput9)

Error correction is a fundamental preprocessing step in many NGS pipelines, in particular for de novo genome assembly. However, existing error correction methods either suffer from high false positive rates since they break reads into independent k-mers or do not scale efficiently to large amounts of sequencing reads and complex genomes. We present CARE - an alignment-based scalable error correction algorithm for Illumina data using the concept of minhashing. Minhashing allows for efficient similarity search within large sequencing read collections which enables fast computation of high-quality multiple alignments. Sequencing errors are corrected by detailed inspection of the corresponding alignments. Our performance evaluation shows that CARE generates significantly fewer false positive corrections than state-of-the-art tools (Musket, SGA, BFC, Lighter, Bcool, Karect) while maintaining a competitive number of true positives. When used prior to assembly it can achieve superior de novo assembly results for a number of real datasets. CARE is also the first multiple sequence alignment based error corrector that is able to process a human genome Illumina NGS dataset in only 4 hours on a single workstation using GPU acceleration. CARE is open-source software written in C ++ (CPU version) and in CUDA/C ++ (GPU version). It is licensed under GPLv3 and can be downloaded at https//github.com/fkallen/CARE. Supplementary data are available at Bioinformatics online. Supplementary data are available at Bioinformatics online. The recent emergence of the novel SARS-coronavirus 2 (SARS-CoV-2) and its international spread pose a global health emergency. The spike (S) glycoprotein binds ACE2 and promotes SARS-CoV-2 entry into host cells. The trimeric S protein binds the receptor using the receptor-binding domain (RBD) causing conformational changes in S protein that allow priming by host cell proteases. Unraveling the dynamic structural features used by SARS-CoV-2 for entry might provide insights into viral transmission and reveal novel therapeutic targets. Using structures determined by X-ray crystallography and cryo-EM, we performed structural analysis and atomic comparisons of the different conformational states adopted by the SARS-CoV-2-RBD. Here, we determined the key structural components induced by the receptor and characterized their intramolecular interactions. We show that κ-helix (polyproline-II) is a predominant structure in the binding interface and in facilitating the conversion to the active form of the S protein. We demonstrate a series of conversions between switch-like κ-helix and β-strand, and conformational variations in a set of short α-helices which affect the hinge region. These conformational changes lead to an alternating pattern in conserved disulfide bond configurations positioned at the hinge, indicating a possible disulfide exchange, an important allosteric switch implicated in viral entry of various viruses, including HIV and murine coronavirus. The structural information presented herein enables to inspect and understand the important dynamic features of SARS-CoV-2-RBD and propose a novel potential therapeutic strategy to block viral entry. Overall, this study provides guidance for the design and optimization of structure-based intervention strategies that target SARS-CoV-2. We have implemented the proposed methods in an R package freely available at https//github.com/Grantlab/bio3d. Supplementary data are available at Bioinformatics online. Supplementary data are available at Bioinformatics online. The human corticotropin-releasing hormone (CRH) test (hCRHtest) is used to differentiate Cushing disease (CD) from ectopic adrenocorticotropin (ACTH) secretion (EAS), to assess autonomous cortisol secretion by the adrenal glands, and to characterize pseudo-Cushing syndrome (CS) or adrenal insufficiency (AI). The