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68 results for “Pangenomics”
Data for: Pangenome analysis reveals local adaptation to climate driven by introgression in oak species
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Pangenomic origins of evolutionary rescue in a staple crop
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Data from: Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets
Background: Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. Results: The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control. Conclusion: The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.
Benchmarking datasets used in the manuscript "Strain-level metagenomic profiling using pangenome graphs with PanTax"
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Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
<p>Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication<br>The data contains two files, namely genome file and genome annotation file:<br>1. Genome:<br>This file contains 12 genomes for 5 species (cultivar), namely: <em>Malus domestica</em> cv. ‘Golden Delicious’ (GD), <em>Malus domestica</em> cv. ‘Gala’ (Gala), <em>Malus domestica</em> cv. ‘Honeycrisp’ (HC), <em>Malus domestica</em> cv. ‘HFTH1’ (HFTH1), <em>Malus baccata</em> (Mba), <em>Malus sieversii</em> (Msi), and <em>Malus sylvestris</em> (Msy)</p> <p>2. Genome annotation:<br>Corresponding to the genome file.<br>Note: Hap1 and hap2 represent two haplotypes of a species (cultivar), all data used for the construction of pan-genomes and comparative genomics analysis.</p>
pangenome-layout-dataset
<p>The archived folder includes the CPU-generated (odgi-layout) and GPU-generated (odgi-layout-gpu) layouts and images for human pangenome chromosomes. <br>It also includes a script to download all the dataset of human pangenome to support the reproduce of the experimental results. </p>
Pangenomes of multiple species for the "Cluster efficient pangenome graph construction with nf-core/pangenome" manuscript.
<p>Pangenomes of multiple species for the "Cluster efficient pangenome graph construction with nf-core/pangenome" manuscript.</p> <p>Each pangenome is represented in a FASTA format file. Each FASTA file was compressed with <em>bgzip</em> and subsequent indices were created with <em>tabix</em>.</p> <p>The name of each file specifies:</p> <ul> <li>The species,</li> <li>and the number of haplotypes.</li> </ul> <p>The built pangenomes graph are represented in GFA format. Each pangenome graph in the paper is uploaded here, too.</p>
Pangenome_benchmark_cuttlefish_length
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Pangenomes of multiple species for the "Building pangenome graphs" publication
<p>Pangenomes of multiple species for the PGGB paper.</p> <p>Each pangenome is represented in a FASTA format file. Each FASTA file is compressed with bgzip so that it can be indexed and directly input to PGGB.</p> <p>The name of each file specifies:</p> <ul> <li>the species;</li> <li>the number of haplotypes;</li> <li>the chromosome.</li> </ul> <p>All sequence names follow the <a href="https://github.com/pangenome/PanSN-spec">PanSN</a> specification.</p> <p>In addition, pangenome graphs (compressed with zstd) are provided for:</p> <p>- the primate chromosome 6;</p> <p>- the E. coli pangenome with 50 haplotypes.</p>
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
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Pangenomic Study During Alcoholic Cirrhosis
ClinicalTrials.gov study NCT01065233. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ANDDI-PRENATOME - Feasibility Study for a " Fast " Pangenomic High Throughput Sequencing Analysis in Prenatal Diagnosis
ClinicalTrials.gov study NCT03964441. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets
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Data from: The Chlamydiales pangenome revisited: structural stability and functional coherence
The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral genes with varying taxonomic distribution and finally 1,125 smaller families. The fact that, even for smaller genomes of Chlamydiales, core genes represent over a quarter of the average protein complement, signifies a certain degree of structural stability, given the wide range of phylogenetic relationships within the group. In addition, the propagation of a corpus of manually curated annotations within the discovered core families reveals key functional properties, reflecting a coherent repertoire of cellular capabilities for Chlamydiales. We further investigate over 2,000 genes without homologs in the pangenome and discover two new protein sequence domains. Our results, supported by the genome-based phylogeny for this group, are fully consistent with previous analyses and current knowledge, and point to future research directions towards a better understanding of the structural and functional properties of Chlamydiales.
Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
<p>Two haplotypes of the T2T genome of Golden Delicious apple and their annotation files</p>
A graph-based goat pangenome reveals structural variations involved in domestication and adaptation
<p>Data are organized as a folder and compressed with tar.gz.</p> <p> </p>
Databases for the Carpentries Pangenomics Workshop
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Pangenome_graph
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Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement
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Kraken2 Human Pangenome Reference Consortium database
<p>A kraken2 database built from the genome assemblies used by the Human Pangenome Reference Consortium (https://projects.ensembl.org/hprc/). This archive contains the three files required by kraken2, hash.k2d, opts.k2d, and taxo.k2d, along with inspect.txt, which is obtained by running kraken2-inspect on the database, ktaxonomy.tsv, which contains the taxonomy information of the database (obtained by running https://github.com/jenniferlu717/KrakenTools#make_ktaxonomypy).</p> <p>The genomes for this database were downloaded using the assembly summary text file included in this dataset and genome_updater.sh (v0.6.3; https://github.com/pirovc/genome_updater)</p> <pre><code>genome_updater.sh -m -a -f "genomic.fna.gz" -t 8 -e "hprc_assembly_summary.txt" -o HPRC_genomes/</code></pre> <p>The python script prepare_kraken_fasta.py was then used to prepare the assemblies for use in kraken with the following command</p> <pre><code>python prepare_kraken_fasta.py -r -T 9606 -o HPRC.fna HPRC_genomes/</code></pre> <p>The database was then built with kraken2 using the following commands</p> <pre><code>kraken2-build --download-taxonomy --db db/ kraken2-build --add-to-library HPRC.fna --db db/ kraken2-build --build --db db/ --threads 16</code></pre>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.