Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,696
datasets available to search
ShareScore release 0.9.0
Dataset results
1,696 results for “DNA sequence”
FIGURE 4 in Description of nymphs and female subimago of Sparsorythus multilabeculatus Sroka & Soldán, 2008 (Ephemeroptera: Tricorythidae) associated with male imago based on DNA sequence data
FIGURE 4. Sparsorythus multilabeculatus, male nymph in dorsal view. Scale bars: 1 mm.
FIGURE 10 in Description of nymphs and female subimago of Sparsorythus multilabeculatus Sroka & Soldán, 2008 (Ephemeroptera: Tricorythidae) associated with male imago based on DNA sequence data
FIGURE 10. Sparsorythus multilabeculatus, male forewing. Scale bar: 1 mm.
FIGURE 5 in Description of nymphs and female subimago of Sparsorythus multilabeculatus Sroka & Soldán, 2008 (Ephemeroptera: Tricorythidae) associated with male imago based on DNA sequence data
FIGURE 5. Sparsorythus multilabeculatus, female nymph in dorsal view. Scale bars: 1 mm.
Fig. 3 in Phylogenetic analysis of the genus Argia Rambur, 1842 (Odonata: Coenagrionidae), based on morphological characters of larvae and mitochondrial DNA sequences
Fig. 3 Phylogenetic hypothesis recovered by Bayesian inference from the total evidence data set
FIGURES 19–30 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 19–30. Neidium vandusenense sp. nov. LM. Fig. 21, holotype. Scale bar = 20 μm.
FIGURES 45–55 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 45–55. Neidium collare sp. nov. LM. Fig. 49, holotype. Scale bar = 20 μm.
FIGURES 69–74 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 69–74. Neidium lavoieanum sp. nov. LM. Fig. 71, holotype. Scale bar = 10 μm.
Linked collectors and determiners for: Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae).
Natural history specimen data linked to collectors and determiners held within, "Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/fa172759-c7a8-4682-b992-8871c155eb3a">https://bionomia.net/dataset/fa172759-c7a8-4682-b992-8871c155eb3a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/fa172759-c7a8-4682-b992-8871c155eb3a">https://gbif.org/dataset/fa172759-c7a8-4682-b992-8871c155eb3a</a>. Formatted as a Frictionless Data package.
FORAlign: Accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on FOur Russians approach with linear space complexity
Open the record for dataset details and reuse information.
Supplementary material 1 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Tables S1–S3
Figure 4 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 4 Maximum likelihood tree for concatenated matrix of all genes. Scale bar: 0.1 units, as estimated by RAXML.
Chart 1 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Chart 1 Support for or against various clades. All columns provide maximum likelihood bootstrap values for or against a particular clade, except for column "8G B," which shows the Bayesian posterior probability estimates for the eight-gene matrix. "8GML" shows the bootstrap values for the eight-gene concatenated matrix, "Nuc G" for the concatenated nuclear genes, "NPC G" for the concatenated nuclear protein-coding genes, and "Mito G" for the concatenated mitochondrial genes. The remaining eight columns provide values for the single gene analyses. All values are expressed as percentages, with positive numbers indicating support for a clade and negative numbers indicating support for a contradictory clade having the highest support. Specific contradictory clades from alternative trees are highlighted in medium grey. Cells with bootstrap values ≥ 90 are shown in black, with values between 75 and 89 in dark grey, and values from 50 to 74 in light grey. Cells in white indicate clades present in the ML tree, but with bootstrap values < 50. Cells in red have bootstrap values for a contradictory clade ≥ 50. Cells in pink have bootstrap values for or against a clade < 50, and the clade is not present in the ML tree. A "-" in a cell indicates that taxon sampling for that gene was not sufficient to assess monophyly of that clade. "#g" shows the number of single-gene analyses (maximum of eight) that support a clade with bootstrap values of 50 or more.
Supplementary material 2 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figures S1–S13
Figure 3 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 3 Habitus images of NebriaAN. (Eonebria) djakonovi Semenov & Znojko BN. (Orientonebria) coreica Solsky CN. (Spelaeonebria) nudicollis Peyerimhoff DN. (Psilonebria) superna Andrewes EN. (Reductonebria) ochotica Sahlberg FN. (Catonebria) banksii Crotch. Scale bars: 1.0 mm. Photograph credits: A, B, F Kiril Makarov; C, D David Maddison; E Alexander Anischenko.
Figure 2 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 2 Habitus images of NebriiniALeistus (Nebrileistus) nubivagus Wollaston BL. (Leistus) ferruginosus Mannerheim CArchastes solitarius (Ledoux & Roux) DNippononebria (Vancouveria) virescens (Horn) ENebria (Oreonebria) castanea Bonelli FN. (Eurynebria) complanata (Linnaeus). Scale bars: 1.0 mm. Photograph credits: A, D–F David Maddison; B, C Alexander Anischenko.
Figure 6 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 6 Summary tree of nebriite phylogeny illustrating the revised classification; clade representation in Europe (including North Africa and the Middle East), Asia, and North America is indicated in the three-box bar.
Figure 5 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 5 Majority rule consensus tree of trees from bootstrap replicates. The first number under a branch is the percentage of bootstrap replicates with that clade, the second number is the estimate of the Bayesian posterior probability of that clade expressed as a percentage.
Figure 1 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 1 Habitus images of NebriitaeANotiokasis chaudoiri Kavanaugh & Nègre BPelophila borealis (Paykull) COpisthius richardsoni Kirby DParopisthius indicus chinensis Bousquet & Smetana ENotiophilus palustris Duftschmid FArchileistobrius hwangtienyuni Shilenkov & Kryzhanovskij. Scale bars: 1.0 mm. Photograph credits: A, C David Maddison; B, E Kiril Makarov; D, F Alexander Anischenko.
Data from: PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data
The pairwise sequentially Markovian coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole-genome data, we here use simulations to investigate its applicability to reference genome-aligned restriction site associated DNA (RAD) data. We find that RAD data can potentially be used for PSMC analysis, but at present with limitations. The key factor is the proportion (p) of the genome that the RAD data covers. In our simulations, a proportion of 10% can still retain a substantial amount of coalescent information, whereas for 1% estimation becomes unreliable. The performance depends strongly on mutation rate (μ) and recombination rate (r) and is proportional to μ*p/r. When the value of this term is low, increasing the amount of data and number of iterations helps restoring the power of the estimation. We subsequently analyse one whole-genome-sequenced and 17 RAD-sequenced three-spined sticklebacks (Gasterosteus aculeatus) from a lake in Greenland. The whole-genome sequence suggests a relatively recent expansion and decline within ca. 4000–40 000 generations ago, possibly reflecting postglacial expansion and founding of the lake population. RAD data, where chromosomes from 10 individuals are combined, identify a similar pattern. Our study provides guidance about the use of PSMC analysis and suggests measures that can improve its utility for RAD data. Finally, the study shows that RAD loci in general contain coalescent information that can be used for developing more targeted methods.
Data from: Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)
Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0-, 12-, 48- and 96-h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12–48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96-h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modified fold coverage values (2- to 16-fold), and additional read-length trimming. We conclude that starting DNA quality is an important consideration for RADSeq; however, the approach remains robust until genomic DNA is extensively degraded.
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.