Ontology highlight
ABSTRACT:
PROVIDER: PRJNA899578 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Great Ape Trio de novo Mutation Rate estimation
| PRJEB29710 | ENA
Project description:In yeast, the extrachromosomal genetic element [KIL-d] alters killer activity of M double stranded RNA killer virus and confers cell resistance against the killer virus. However, its underlying mechanism and the molecular nature of [KIL-d] is unknown. We found [KIL-d] selectively increases the rate of de novo mutation in the killer toxin gene of the viral genome. To verify this hypotesis, we performed deep sequence analysis to calculate mutation rate.
2015-10-16 | E-MTAB-3932 | biostudies-arrayexpress
Project description:De novo peptide sequencing is a fundamental research area in mass spectrometry (MS) based proteomics. However, those methods have often been evaluated using a couple of simple metrics that do not fully reflect their overall performance. Moreover, there has not been an established method to estimate the false discovery rate (FDR) and the significance of de novo peptide-spectrum matches (PSMs). Here we propose NovoBoard, a comprehensive framework to evaluate the performance of de novo peptide sequencing methods. The framework consists of diverse benchmark datasets (including tryptic, nontryptic, immunopeptidomics, and different species), and a standard set of accuracy metrics to evaluate the fragment ions, amino acids, and peptides of the de novo results. More importantly, a new approach is designed to evaluate de novo peptide sequencing methods on target-decoy spectra and to estimate their FDRs. Our results thoroughly reveal the strengths and weaknesses of different de novo peptide sequencing methods, and how their performances depend on specific applications and the types of data. Our FDR estimation also shows that some tools may perform better than the others in distinguishing between de novo PSMs and random matches, and can be used to assess the significance of de novo PSMs.
2024-08-28 | PXD055277 | Pride
Project description:<p> This study is part of the '<i>First 1,000 Days of Life and Beyond</i>' study at the Inova Translational Medicine Institute. Whole-genome sequencing data from 1,291 parent-offspring trios was used to study the properties of clustered <i>de novo</i> mutations. The maternal clusters were found to be enriched in regions with accelerated maternal mutation rate and show distinct mutational signatures. </p> <p>For additional details, please refer to: "<i>Germline de novo mutation clusters arise during oocyte aging in genomic regions with increased double-strand break incidence</i>". Jakob M. Goldmann, Vladimir B. Seplyarskiy, Wendy S.W. Wong, Thierry Vilboux, Pieter B. Neerincx, Dale L. Bodian, Benjamin D. Solomon, Joris A. Veltman, John F. Deeken, Christian Gilissen, John E. Niederhuber. <a href="https://www.ncbi.nlm.nih.gov/pubmed/29507425">Nature Genetics</a>. </p>
| phs001522 | dbGaP
Project description:Estimation of the spontaneous mutation rate in Heliconius melpomene
| PRJEB7581 | ENA
Project description:De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background. We analyzed CNVs in seven cloned dogs using the nuclear donor genome as reference by array-CGH
2013-12-17 | E-GEOD-49092 | biostudies-arrayexpress