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Filename: models/Detail_model.php
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Function: strpos
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Function: insertAPISummary
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Filename: controllers/Detail.php
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We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
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http://dx.doi.org/10.1038/nbt.3886 | DOI Listing |
Front Genet
December 2024
Research Group Animal Immunogenomics, CEITEC - VETUNI Brno, Brno, Czechia.
Manul () is the only representative of the genus which makes up the Leopard Cat lineage along with the genus . Their habitat is characterized by harsh environmental conditions. Although their populations are probably more stable than previously thought, it is still the case that their population size is declining.
View Article and Find Full Text PDFLab Med
December 2024
Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, United States.
Background: CALR mutation analysis is routinely used to diagnose BCR/ABL1-negative myeloproliferative neoplasms. The 2 most common CALR mutations are a 52-base pair (bp) deletion and a 5-bp insertion, which account for approximately 85% of cases.
Methods: To evaluate our new microfluidic chip assay, we tested CALR mutant and wild-type specimens that were previously analyzed using conventional methods at a reference laboratory.
Sci Data
December 2024
School of Pharmaceutical Sciences, Xiamen University, 4221 Xiangannan road, Xiamen, 361104, China.
Pyrosomes represent a group of marine holozooplankton. They do not exist as individual entities but as intricate colonies comprising numerous zooids, well-known for their bioluminescent properties. Pyrosomes inhabit most oceanic waters spanning tropical to temperate regions.
View Article and Find Full Text PDFNPJ Genom Med
December 2024
Experimental Center of Clinical Research, the First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
Wilson's disease (WD) typically manifests in children and young adults, with little knowledge of its late-onset forms. In this study, we performed a retrospective cohort study of 105 WD patients (99 index cases, 6 siblings) with an onset age ≥35 years. We compared 99 index late-onset patients with 1237 early-onset patients and analyzed the ATP7B variant penetrance referring to the Genome Aggregation Database (gnomAD).
View Article and Find Full Text PDFBioinformatics
December 2024
Max-Planck-Institute for Biology Tübingen, Department of Molecular Biology, Tübingen, Germany.
Motivation: As genome graphs are powerful data structures for representing the genetic diversity within populations, they can help identify genomic variations that traditional linear references miss, but their complexity and size makes the analysis of genome graphs challenging. We sought to develop a genome graph analysis tool that helps these analyses to become more accessible by addressing the limitations of existing tools. Specifically, we improve scalability and user-friendliness, and we provide many new statistics tailored to variation graphs for graph evaluation, including sample-specific features.
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