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19,342 results for “Sequence”
Treponema pallidum Cytoplasmic filament protein gene partial sequence
<p>A partial sequence of the Cytoplasmic filament protein gene (cfpA) of treponema pallidum from non human primates</p>
Sequencing data from: Divergent lineages in a young species: the case of Datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula
<div> <div> <p><strong>Premise: </strong>Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial–interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is <em>Yucca</em>, with <em>Y. valida</em> having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence.<br>Methods: We assembled 4411 SNPs from 147 plants of <em>Y. valida</em> throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species.<br>Results: Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of <em>Y. valida</em> and its sister species.<br>Conclusions: Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in <em>Y. valida</em>.</p> </div> </div>
Tif Image Stack - Example of a long sequence that was split into two tif files
<p>These two tif files were recorded during a single time-series capture. </p> <p>20240723_uro3g_t000000.tif - This image stack contains 3984 frames (time slices)</p> <p>20240723_uro3g_t000001.tif - This image stack contains 324 frames (time slices).</p> <p>The total number of frames/time slices should be 4308. (3984 + 324)</p> <p> </p> <p> </p> <p> </p>
Intra-host single-genome sequences of SARS-CoV-2 spike from people without HIV and people living with HIV
<p>Supporting data and code for the study "Rapid Intra-host Diversification and Evolution of SARS-CoV-2 in Advanced HIV Infection" (2024) by Ko & Radecki et al.</p> <p>See <a href="https://github.com/niaid/UMI-pacbio-pipeline/releases/tag/SC2-HIV-demo">the GitHub</a> for demo of SGS and haplotype generation using example data from the study.</p> <p>Raw sequencing data are deposited at <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1055920">PRJNA1055920</a>.</p> <p>READMEs are available within individual folders and releases.</p>
Fig. 1 in Genetic diversity of Halyomorpha halys (Hemiptera, Pentatomidae) in Korea and comparison with COI sequence datasets from East Asia, Europe, and North America
Fig. 1. Halyomorpha halys collection sites in Korea and the USA.
MMSEQS meets AntiRef90: reference clusters of human antibody sequences
<p>This data set contains pre-computed mmseqs databases for the antiref fasta files created by <em>Briney et al.</em> </p> <p>Please cite the original work if you use any of the databases provided here.</p> <p>Sources:</p> <ul> <li><a href="https://github.com/brineylab/antiref">Antiref GitHub</a></li> <li><a href="../records/7474336">Antiref Zenodo</a></li> <li><a href="https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad109/7247530?login=true">Antiref Paper</a></li> </ul> <p> </p> <p>The mmseqs databases were created as follows:</p> <p> </p> <p>```</p> <p>aria2x -x16 -s16 --input-file antiref_links.txt<br>snakemake -s antiref_mmseqs.smk --jobs 1 --cores 1 --local-cores 250</p> <p>```</p> <p> </p> <p>Please check the summary repository for the fasta files and snakemake files. In this sub repo we only store the antiref files matching the title of the repo.</p> <p> </p>
Fig. 6 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing
Fig. 6. Bar chart of the relative abundances of genera.
Fig. 8 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing
Fig. 8. Bar chart of the relative abundances of bacteria.
Fig. 3 in New data on Thelohanellus nikolskii Achmerov, 1955 (Myxosporea, Myxobolidae) a parasite of the common carp (Cyprinus carpio, L.): The actinospore stage, intrapiscine tissue preference and molecular sequence
Fig. 3. Thelohanellus cysts on the scales of an aged common carp specimen.
Fig. 1 in The neglected diversity: Description and molecular characterisation of Trypanosoma haploblephari Yeld and Smit, 2006 from endemic catsharks (Scyliorhinidae) in South Africa, the first trypanosome sequence data from sharks globally
Fig. 1. Map of sampling sites on the south coast of South Africa.
Fig. 1 in New data on Thelohanellus nikolskii Achmerov, 1955 (Myxosporea, Myxobolidae) a parasite of the common carp (Cyprinus carpio, L.): The actinospore stage, intrapiscine tissue preference and molecular sequence
Fig. 1. Thelohanellus nikolskii cysts on the fins of carp fingerlings.
CodonTransformer - Genomic and CodonTransformer-Generated Sequences for Fine-tuned Organisms
<p>This dataset is used in creating Fig. 2a and Supplementary Figs. 2-16 of the paper, mainly including the predictions of base (pretrained) and finetuend CodonTransformer model along with various metrics. </p>
Phylogenetic tree of 1819 YfaL protein sequences identified in 2053 E. coli genomes.
<p><strong><span>Phylogenetic tree of 1819 YfaL protein sequences identified in 2053 <em>E. coli</em> genomes. </span></strong><span>The purple circles on the branches represent bootstrap values > 0.8. The different strain’s phylogroups are displayed outside of the tree.</span></p>
Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae)
<p><span>The sugarcane aphid, <em>Melanaphis sacchari</em> (Zehntner, 1897), is an agricultural pest that causes damage to plants in the <a name="OLE_LINK12"></a>Poaceae (the grasses) family, such as sorghum and sugarcane. However, genomic resources of this species are currently limited. Here, we used Nanopore long reads and Hi-C interaction map to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the three autosomes and the X chromosome. <a name="OLE_LINK4"></a>Repetitive sequences accounted for 16.29% of the chromosomes and a total of 12,350 protein-coding genes were annotated, achieving 95.8% benchmarking universal single-copy orthologs (BUSCO) gene completeness. Phylogenomic analysis by comparing <em>M. sacchari</em> with twenty-four published aphid genomes representing three aphid tribes reveals that <em>M. sacchari</em> belongs to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. <span>T</span>he genomic resources reported in this study will be useful for understanding the evolution of aphid genomes and studying pest management of <em>M. sacchari</em>.</span></p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "A new glassfrog of the genus Nymphargus (Anura: Centrolenidae) from Cordillera del Cóndor, Ecuador"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "<span>A new glassfrog of the genus Nymphargus</span> (Anura<span>:</span> Centrolenidae) <span>from Cordillera del Cóndor, Ecuador</span>"</p> <p>The matrix is in NEXUS format and has 6613 bp and 102 terminals.</p> <p>Partitions are as follows:</p> <div> <div>charset 12S = 1-944;</div> <div>charset 16S = 945-2093;</div> <div>charset BNDFcodonPos1 = 2096-2792\3;</div> <div>charset BNDFcodonPos2 = 2094-2793\3;</div> <div>charset BNDFcodonPos3 = 2095-2791\3;</div> <div>charset ND1codonPos1 = 2795-3749\3;</div> <div>charset ND1codonPos2 = 2796-3750\3;</div> <div>charset ND1codonPos3 = 2794-3751\3;</div> <div>charset CXCR4codonPos1 = 3753-4107\3;</div> <div>charset CXCR4codonPos2 = 3754-4105\3;</div> <div>charset CXCR4codonPos3 = 3752-4106\3;</div> <div>charset cmyccodonPos1 = 4108-4507\3;</div> <div>charset cmyccodonPos2 = 4109-4508\3;</div> <div>charset cmyccodonPos3 = 4110-4509\3;</div> <div>charset POMCcodonPos1 = 4511-5120\3;</div> <div>charset POMCcodonPos2 = 4512-5121\3;</div> <div>charset POMCcodonPos3 = 4510-5122\3;</div> <div>charset RAG1codonPos1 = 5123-5576\3;</div> <div>charset RAG1codonPos2 = 5124-5577\3;</div> <div>charset RAG1codonPos3 = 5125-5578\3;</div> <div>charset SLC8A1codonPos1 = 5580-6120\3;</div> <div>charset SLC8A1codonPos2 = 5581-6118\3;</div> <div>charset SLC8A1codonPos3 = 5579-6119\3;</div> <div>charset SLC8A3codonPos1 = 6122-6587\3;</div> <div>charset SLC8A3codonPos2 = 6123-6585\3;</div> <div>charset SLC8A3codonPos3 = 6121-6586\3;</div> </div>
Fig. 2 in Allopatric chromosomal variation in Nematocharax venustus Weitzman, Menezes & Britski, 1986 (Actinopterygii: Characiformes) based on mapping of repetitive sequences
Fig. 2. Representative karyotype of Nematocharax venustus. Bar = 5 µm.
FIGURE 7 in Graphic correlation of the upper Eifelian to lower Frasnian (Middle-Upper Devonian) conodont sequences in the Spanish Central Pyrenees and comparison with composite standards from other areas
FIGURE 7. Correlation of the three sections based on the results of the graphic correlation method.
FIGURE 9 in Deciduous dentition and dental eruption sequence of Bothriogenys fraasi (Anthracotheriidae, Artiodactyla) from the Fayum Depression, Egypt
FIGURE 9. Comparison of the different stages (I-V) of the eruption sequence of Bothriogenys fraasi.
1200 artificial genome sequences containing a single-or-multistep NAHR event each.
<p>This is a companion dataset to Höps et al. 2024: <strong>Impact and characterization of serial structural variations across humans and great apes</strong></p> <p> </p> <p>600 'ancestor'; i.e. source sequences with two pairs of SDs were mutated first. The SD sequences of the two pairs are not overlapping, however the space between SD pairs IS. There are two possible configurations for this: 1-2-2-1 or 1-2-1-2, with 1 and 2 denoting the identity of repeat pair 1 and 2. This configuration as well as the relative orientation of the two SDs (same direction / inverse direction) were randomly chosen.</p> <p>We used four target SD lenghts [100bp, 500bp, 1000bp, 10000bp] and three SD similarity scores [90%, 95%, 99%], totalling 12 combinations. Here, we created 50 artifical sequences for each of these configurations, totalling 600 sequences. </p> <p>From the 600 ancestor sequences, we then simulated several, again randomly chosen NAHR chains up to depth-3 using the mutate_sequences.py script in the attached github. Finally, we chose two 'representative' mutated seuqnces for each ancestor, totalling 1200 sequences published here. </p> <p>This upload contains two (zipped) folders; ancestors and mutated_seqs. The ancestors are enumerated 1-600, and mutated seqs likewise have their corresponding ancestor in the beginning of their filename. </p> <p>The data was created using the generate_mutate script in https://github.com/WHops/nahrwhals_simulate_events release v0.2. </p> <p> </p> <p>contact: wolfram.hoeps@gmail.com</p>
Flow Cytometry Data from "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing"
<p>This record contains the flow cytometry data from the manuscript "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing."</p> <p>Files are in <a href="https://docs.flowjo.com/flowjo/advanced-features/fj-acs/">Archive Cytometry Standard (ACS) format</a> . Each <code>.acs</code> file is a zip container which holds both the raw <code>.fcs</code> files and a FlowJo workspace (<code>.wsp</code>) file.</p> <p>Keywords in the workspace file identify which primary antibody (<code>primary</code>) was used and which cell genotype (<code>strain</code>) was used for each sample. The workspace also encodes the gating scheme and compensation matrix applied to each sample. Plots in the manuscript are exported from Layout views in the workspace.</p>
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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.