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19,342 results for “sequence”
Aligned DNA sequence matrix for phylogenetic analyses in the article "Systematics of the Dendropsophus leucophyllatus species group (Anura, Hylidae) from the Chocó region of Ecuador, with description of a new species"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of the <em>Dendropsophus leucophyllatus</em> species group (Anura, Hylidae) from the Chocó region of Ecuador, with description of a new species"</p> <p>The matrix is in NEXUS format and has 7691 bp and 203 terminals.</p> <p>Partitions are as follows:</p> <div> <div>charset 12S = 1-996;</div> <div> </div> <div>charset CO1codonPos1 = 997-1639\3;</div> <div>charset CO1codonPos2 = 998-1640\3;</div> <div>charset CO1codonPos3 = 999-1638\3;</div> <div> </div> <div>charset ND1nonCoding = 1641- 1713 2675- 2796 ;</div> <div>charset ND1codonPos1 = 1714-2674\3;</div> <div>charset ND1codonPos2 = 1715-2672\3;</div> <div>charset ND1codonPos3 = 1716-2673\3;</div> <div> </div> <div>charset CytbcodonPos1 = 2798-3686\3;</div> <div>charset CytbcodonPos2 = 2799-3687\3;</div> <div>charset CytbcodonPos3 = 2797-3685\3;</div> <div> </div> <div>charset RhodcodonPos1 = 3689-4001\3;</div> <div>charset RhodcodonPos2 = 3690-4002\3;</div> <div>charset RhodcodonPos3 = 3688-4003\3;</div> <div> </div> <div>charset TYRcodonPos1 = 4005-4539\3;</div> <div>charset TYRcodonPos2 = 4006-4537\3;</div> <div>charset TYRcodonPos3 = 4004-4538\3;</div> <div> </div> <div>charset RAG1codonPos1 = 4542-4965\3;</div> <div>charset RAG1codonPos2 = 4540-4966\3;</div> <div>charset RAG1codonPos3 = 4541-4964\3;</div> <div> </div> <div>charset POMCcodonPos1 = 4967-5441\3;</div> <div>charset POMCcodonPos2 = 4968-5439\3;</div> <div>charset POMCcodonPos3 = 4969-5440\3;</div> <div> </div> <div>charset SIAH1codonPos1 = 5443-5836\3;</div> <div>charset SIAH1codonPos2 = 5444-5837\3;</div> <div>charset SIAH1codonPos3 = 5442-5838\3;</div> <div> </div> <div>charset 16S_rec = 5839-7695;</div> </div>
Symbiochlorum biodiversity based on strains and environmental sequences
<p>Datasets associated with the publication of biodiversity discovery in the Symbiochlorum lineage based on new culture strains and environmental sequence data mining.</p> <p>1. V4 ASV sequences<br>2. V9 ASV sequences</p> <p>3. partial 18S sequences from transcriptome</p> <p>4. full length 18S alignments with V4 added<br>5. full length 18S alignments with V9 added</p> <p>6. trimmed alignment V4 Symbiochloraceae used for distance calculation<br>7. trimmed alignment V9 Symbiochloraceae used for distance calculation</p> <p>8. original tree V4<br>9. original tree V9</p> <p> </p>
Sequence and functional analyses of native plasmids from plant pathogenic Gammaproteobacteria: comparative genomics, conjugative mobilization and fitness effects
<p>These data tables are part of the Supplementary Material for Chapter I of the thesis titled <em>"Sequence and Functional Analyses of Native Plasmids from Plant-Pathogenic Gammaproteobacteria: Comparative Genomics, Conjugative Mobilization, and Fitness Effects."</em></p>
Draft Genome Sequences of 38 Aspergillus parasiticus isolates
Open the record for dataset details and reuse information.
Supplementary material for "Stellar flare morphology with TESS across the main sequence"
<p>Online material for the paper titled "Stellar flare morphology with TESS across the main sequence". The dataset includes the manually flagged TESS light curves used to train the <em>flatwrm2</em> flare detection algorithm (<a href="https://github.com/vidakris/flatwrm2" target="_blank" rel="noopener">https://github.com/vidakris/flatwrm2</a>), the final manually vetted flare catalog, the extracted flare profiles, and Jupyter notebooks demonstrating how the data can be used.</p> <h2>Files</h2> <ul> <li><strong>flatwrm2_training_set.tar.gz</strong>: TESS 2-min cadence light curves used to train <em>flatwrm2</em> for flare detection. All files contain three columns, time in TBJD, PDCSAP flux, and a 1/0 flag for flare/not flare. Files are sorted into three directories:<br> <ul> <li>active_stars: Selected active stars up to sector 40 for the original training set of <em>flatwrm2</em>, 208 light curves.</li> <li>random_sample: Random stars up to sector 40 for the original training set of <em>flatwrm2</em>, 8000 light curves. Only a small fraction of them is flaring.</li> <li>new_selection: New selection of stars up to sector 69, 4631 light curves. It includes flaring and non-flaring stars, and also known astrophysical false positives (e.g., RR Lyrae stars). See Sect. 2.2 of the paper for details.</li> </ul> </li> <li><strong>Table2_flaring_star_catalog.csv</strong>: Catalog of flaring stars (Table 2 in the paper)</li> <li><strong>Table3_flare_catalog.csv</strong>: TESS flare catalog, including only the correctly extracted flares, with the same length as TESS_flare_shapes.dat (Table 3 in the paper)</li> <li><strong>Table3_flare_catalog_not_extracted.csv</strong>: Continuation of the TESS flare catalog, including only the incorrectly extracted flares (Table 3 in the paper). As most calculated parameters are probably erroneous, only the flare peak times are reported.</li> <li><strong>TESS_flare_shapes.dat</strong>: Scaled and interpolated TESS flare shapes, one flare profile for each entry in Table3_flare_catalog.csv</li> <li><strong>TESS_original_flare_shapes_time.dat</strong>: Times for the scaled, but not interpolated flares</li> <li><strong>TESS_original_flare_shapes_flux.dat</strong>: Fluxes for the scaled, but not interpolated flares</li> <li><strong>Table6_solar_flare_catalog.csv</strong>: Solar flare parameters from SDO/EVE (Table 6 in the paper). <em>Note:</em> the SDO/EVE data products have a version number in the URL. We used version 7 for the analysis, but it can change after major updates in the SDO data processing pipeline. Please change the URL accordingly, if you have issues accessing the data (e.g., 007 --> 008).</li> <li><strong>solar_flare_shapes.dat</strong>: Scaled and interpolated solar flare profiles from SDO/EVE, one flare profile for each entry in Table6_solar_flare_catalog.csv</li> <li><strong>01_Loading_data.ipynb</strong>: A Jupyter notebook demonstrating how the above datasets can be used</li> <li><strong>02_Sampling_flare_shapes.ipynb</strong>: A Jupyter notebook demonstrating how flare shapes can be sampled (Sect. 4.2 in the paper)</li> <li><strong>03_Locating_similar_flares.ipynb</strong>: A Jupyter notebook demonstrating how flares similar to an input shape can be located in the catalog (Sect. 4.3 in the paper)</li> </ul>
Source data of the MultiSTAAR manuscript "A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies".
<p>This dataset serves as the source data for Figures 2-3 and Extended Data Figures 1-2 of the MultiSTAAR manuscript titled "A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies". MultiSTAAR is a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies.<br><br><strong>Figure 2.</strong> Manhattan plots and Q-Q plots for unconditional gene-centric coding, noncoding and ncRNA multi-trait analysis of low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerids (TG) using TOPMed data (<em>n</em> = 61,838).<br><br><strong>Figure 3.</strong> TOPMed genetic region (2-kb sliding window) unconditional multi-trait analysis results of low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TG) using TOPMed data (<em>n</em> = 61,838).<br><br><strong>Extended Data Figure 1.</strong> Manhattan plots and Q-Q plots for unconditional gene-centric coding, noncoding and genetic region (2-kb sliding window) multi-trait analysis of fasting glucose (FG) and fasting insulin (FI) using TOPMed data (<em>n</em> = 21,731).<br><br><strong>Extended Data Figure 2.</strong> Manhattan plots and Q-Q plots for unconditional gene-centric coding, noncoding and genetic region (2-kb sliding window) multi-trait analysis of C-reactive protein (CRP), interleukin 6 (IL-6), lipoprotein-associated phospholipase A2 (Lp-PLA2) activity, and lipoprotein-associated phospholipase A2 (Lp-PLA2) mass using TOPMed data (<em>n</em> = 9,380).</p>
Whole genome re-sequencing workshop data: fastq files and reference genomes
<p> </p> <p>Whole genome re-sequencing data analysis workshop datasets. The files are necessary inputs for the workshop in https://github.com/PoODL-CES/Genomics_learning_workshop</p> <p>Tools and scripts listed in the https://github.com/PoODL-CES/Genomics_learning_workshop repository.</p> <p> </p> <p>These are subsampled fastq files from:<br><br>Khan, A., Patel, K., Shukla, H., Viswanathan, A., van der Valk, T., Borthakur, U., Nigam, P., Zachariah, A., Jhala, Y.V., Kardos, M. and Ramakrishnan, U., 2021. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. <em>Proceedings of the National Academy of Sciences</em>, <em>118</em>(49), p.e2023018118.</p> <p>The reference genome is from :</p> <p>Shukla, H., Suryamohan, K., Khan, A., Mohan, K., Perumal, R.C., Mathew, O.K., Menon, R., Dixon, M.D., Muraleedharan, M., Kuriakose, B. and Michael, S., 2023. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. <em>GigaScience</em>, <em>12</em>, p.giac112.</p> <p> </p> <p>The reference has been indexed using:</p> <p>bwa index <a target="_blank" rel="noopener noreferrer">GCA_021130815.1_PanTigT.MC.v3_genomic.fna</a></p> <p> </p>
Bins with greater than 50% completeness and less than 10% contamination from the paper "Benchmarking Metagenomic Binning Tools on Real Datasets Across Sequencing Platforms and Binning Modes".
<p>These bins, which exhibit greater than 50% completeness and less than 10% contamination, including MQ, NC, and HQ bins, were recovered from seven different data-binning combinations across five real-world datasets.</p> <p>CheckM2 results for the bins generated from each sample were also provided to corroborate the findings.</p> <p>Completeness and contamination were evaluated using CheckM 2 (version 1.0.2). We noted that the results from running CheckM2 may exhibit slight variations, but these differences do not affect the overall assessment.</p>
FIGURE. Comparison of the sequences of the internal transcribed spacer (ITS) region of Hedysarum sunhangii and Hedysarum nuratense. The variable region is shown in a red frame. in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Comparison of the sequences of the internal transcribed spacer (ITS) region of Hedysarum sunhangii and Hedysarum nuratense. The variable region is shown in a red frame.
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches. in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches.
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches
BactPrep: A user-friendly whole-genome sequencing analysis platform for the detection of homologous recombination and horizontal gene transfer in bacteria - Sample Dataset
<p>This is the dataset used as the sample dataset for the pipeline BactPrep. This dataset consists of 218 <em>Streptococcus pneumoniae</em> PMEN1 WGS assemblies collected from the year 1984 - 2008 from 22 unique countries globally. The raw sequencing data was originally published in the work: Rapid pneumococcal evolution in response to clinical interventions (doi: 10.1371/journal.ppat.1002745) under the bioproject PRJEB2085.</p> <p>We have assembled the raw sequences records with the following steps: 1) raw reads were first quality checked using fastQC 0.11.9; 2) adapters and low quality reads were removed using Trimmomatic 0.39 with parameter “ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”; 3) trimmed reads were error-corrected and assembled into WGS assemblies using SPAdes 3.15.0 with parameters "--careful --mismatch-correction”.</p>
Heme oxygenase pfam14518 sequence similarity network
<p>Sequence similarity network generated from pfam14518 using the EFI-GNT webtool. Each node is representative of sequences that are 80% identical. </p>
Targeted Next Generation Sequencing data for European Green Crab
<p class="western"><span>In the northeast Pacific Ocean there is high interest in developing eDNA-based survey methods to aid management of invasive populations of European green crab (<i>Carcinus maenas</i>). Expected benefits are improved sensitivity for early detection of secondary spread and to assess the outcome of eradication efforts. A new eDNA-based approach we term 'Targeted Next Generation Sequencing (tNGS)' is introduced here and shown to improve detection relative to qPCR at sites with lower green crab CPUE values measured by trapping. DNA standards (gBlock) with starting molecule copies that were 10- to 100- times lower than the qPCR limit of detection returned significant numbers of sequencing reads, which in our field assessments translated to a 7% - 10% increase in detection probability from tNGS relative to qPCR at sites with lower CPUE. We also found the number of sequencing reads from tNGS was significantly correlated with green crab CPUE whereas Ct values from qPCR were not. When sources of variation were partitioned for each assay, we found the difference between mean within-site and mean between-site variation was much larger and had non-overlapping confidence intervals for tNGS relative to qPCR, suggesting the former may offer more power for detecting spatial variation in eDNA availability. Results presented here indicate this approach is suitable for species of known low abundances where a positive detection has high economic or environmental consequences. Any species with an existing qPCR assay can be easily tested with a tNGS assay. We conclude with a discussion on the fit for purpose applications of tNGS vs. qPCR on how to best apply molecular surveys in management programs.</span></p>
Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex
<p>This contains data for the manuscript: "Illumina Whole Genome Sequencing indicates Ploidy Level Differences within the <i>Valenzuela flavidus </i>(Psocodea: Psocomorpha: Caeciliusidae) Species Complex".</p> <p><i>Valenzuela flavidus</i> is a species of bark louse which is known to have asexual parthenogenetic populations in Europe but is believed to have sexual and asexual populations in North America as well. Historically, <i>Valenzuela aurantiacus</i> was the species epithet recognized for North American members until reports of asexual reproduction surfaced in certain North American populations. Cytogenetic studies have demonstrated European all-female populations are triploid. However, males are often reported in North America suggesting diploidy for sexual populations. With the use of Illumina whole genome sequencing, genetic diversity among North American and European populations was explored with phylogenomic methods. Ploidy level was estimated by examining allele frequencies of read-mapped homologous gene regions. Results indicate divergent populations between Europe and North America. North American populations containing males are estimated to be diploid suggesting a different mechanism of genomic reproduction. These results suggest divergent population structure among European asexual and North American sexual members of <i>V. flavidus</i> providing insight for future studies to understand patterns of asexuality reported within the complex.</p> <p>The following file contains all gene alignments, concatenated supermatrix, and mitochondrial alignment for this manuscript. In addition, the BAM files used to estimate allele frequencies. Also, gene trees for coalescent analysis, resultant treefiles from IQ-tree searches, and MCMCtree result.</p>
Nucleotide sequences in Procambarus clarkii
<p>Crayfish is a model for studying the effect of light on locomotor activity and neuroendocrine functions. In this study, we have described 62 transcripts from the pleonal nerve cord of the crayfish, using bioinformatics tools that identify phylogenetic families of genes related to the light interaction in the extraretinal photoreceptors. We deposited all sequencing data in the GenBank database. Here shows supplemental data from the freshwater crayfish <i>Procambarus clarkii</i>. The results suggest that the genes related to ocular and extraocular light perception in the crayfish <i>P. clarkii</i> use common biosynthesis pathways and phototransduction cascades.</p>
Figure 16 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology
Figure 16. Nine species of Paramormyrops from Lower Guinea showing, from left to right, head shape viewed from above, the outline of the body, and representative female and male EOD waveforms. Head shapes are camera lucida tracings of the holotypes for each species from the snout to end of opercular opening. The first six have sharp V-shaped head profiles and the last three have relatively blunt U-shaped heads. All but the last two have electric organs composed of Type NPp electrocytes (exhibiting Non-Penetrating stalks innervated on the posterior face). The last two have electric organs composed of Type Pa electrocytes (with Penetrating stalks innervated on the anterior face). All known mormyrids with Type Pa electrocytes have an initial, head-negative peak, P0, in the EOD waveform as illustrated here for P. kingsleyae. The P0 peak is absent in all species with Type NPp electrocytes. The EOD of P. batesii is unknown, but the electric organ is composed of Type Pa electrocytes.
Figure 9 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology
Figure 9. Histology of para-sagittal section of paralectotype of P. sphekodes specimen MNHN 1998-1050 (Female, 98.7 mm, SL) shows electrocytes of type NPp (Non-Penetrating stalks with posterior innervation). The specimen, collected from Doumé Falls by Alfred Marche in 1876–1877 and preserved in alcohol, was embedded in plastic, sectioned with a tungsten carbide knife at 7 µm and stained with toluidine blue. E = main body of the electrocyte; anterior = anterior face of electrocyte; post = posterior face of same electrocyte; c = collagen layer separating two electrocytes; S = stalk of electrocyte which is innervated by the axons from the electromotor nerve (not shown); s = stalklets, or small branches from a dividing stalk that eventually fuse with posterior face of the electrocyte. Stalks are innervated on the posterior side of the electrocyte and all branches of the stalk system remain posterior to the main body of the electrocyte without crossing to the opposite or anterior side.
Figure 11 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology
Figure 11. (A, B) Collection localities near the rapids at Doumé (0.84245°S, +12.96249°E) on the Ogooué River of Gabon, where P. sphekodes is sympatric with P. ntotom sp. nov. (B) shows local villagers fishing with hoop nets at Doumé. (C, D) View of the Sébé River (0.93494°S, 13.35767°E) where the two species are also sympatric. Both habitats are moderate-sized rivers with gentle flow or rapids over rocky outcroppings, interspersed with sandy beaches, surrounded by dense rain forest. The Ogooué River is 75–100 m wide at Doumé, 3 m in depth, and the water had low conductivity (13.9 µs/cm) at pH 7.04 and 6.66 mg/L O2 (83.1% saturated) at 26.7 °C. The Sébé River is 55–75 m wide, approximately 3.1 m deep, 16.0 µs conductivity, 7.08 pH and 7.5 mg/L O2 (93.6% saturation) at 26.6°C).
Figure 12 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology
Figure 12. Holotype of P. ntotom sp. nov. CUMV 98138, tag number JPS-1189, male, 178 mm SL, from top to bottom photographed when alive, preserved in alcohol left and right sides, and radiograph. Scale bars = 1 cm.
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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.