G3 (Bethesda)
Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China.
Published: November 2024
Genome assembly errors can have a profound effect on downstream analyses. Collinearity-based Assembly Correction Tool (CATG) is designed to rectify these errors by leveraging collinearity information between the assembled genome and a reference genome. CATG provides a user-friendly interface for visualizing and manually correcting assembly errors. It supports various operations such as insertion, deletion, inversion, and swapping of contigs and chromosomes. The software automatically re-clusters, re-labels, and re-draws the assembly after each modification, ensuring that users can easily track changes. CATG is a robust tool designed to efficiently correct large-scale assembly errors in polyploid genomes, featuring advanced collinearity detection capabilities.
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http://dx.doi.org/10.1093/g3journal/jkae277 | DOI Listing |
PeerJ
January 2025
Department of Computer Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.
Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality.
View Article and Find Full Text PDFSoft Matter
January 2025
Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT 06510, USA.
Hydrogels are popular platforms for cell encapsulation in biomedicine and tissue engineering due to their soft, porous structures, high water content, and excellent tunability. Recent studies highlight that the timing of network formation can be just as important as mechanical properties in influencing cell morphologies. Conventionally, time-dependent properties can be achieved through multi-step processes.
View Article and Find Full Text PDFPLoS Genet
January 2025
Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India.
During chromosome segregation, the spindle assembly checkpoint (SAC) detects errors in kinetochore-microtubule attachments. Timely activation and maintenance of the SAC until defects are corrected is essential for genome stability. Here, we show that shugoshin (Sgo1), a conserved tension-sensing protein, ensures the maintenance of SAC signals in response to unattached kinetochores during mitosis in a basidiomycete budding yeast Cryptococcus neoformans.
View Article and Find Full Text PDFPulsed Dipolar ESR Spectroscopy (PDS) is a uniquely powerful technique to characterize the structural property of intrinsically disordered proteins (IDPs) and polymers and the conformational evolution of IDPs and polymers, e.g. during assembly, by offering the probability distribution of segment end-to-end distances.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Life Science and Medical Bioscience, Laboratory of Cytoskeletal Logistics, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan.
In mammalian epithelial cells, cytoplasmic microtubules are mainly non-centrosomal, through the functions of the minus-end binding proteins CAMSAP2 and CAMSAP3. When cells enter mitosis, cytoplasmic microtubules are reorganized into the spindle composed of both centrosomal and non-centrosomal microtubules. The function of the CAMSAP proteins upon spindle assembly remains unknown, as these do not exhibit evident localization to spindle microtubules.
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