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61 results for “sequence similarity”
Fig. 6 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes
Fig. 6 Correlations of diversity indices obtained with microscopy and HTS. All correlations are significant and follow linear models (see Table 1)
Fig. 2 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes
Fig. 2 Correlation between both distance matrices (Bray-Curtis distances) calculated between diatom compositions of samples obtained with microscopy and HTS
Fig. 5 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes
Fig. 5 Comparison of diversity indices obtained with microscopy and HTS. Classes boundaries for α diversity: c1 <0.675 ≤ c2 <1.100 ≤ c3 <1.525 ≤ c4 <1.950 ≤ c5 <2.375 ≤ c6 <2.800 ≤ c7 <3.225 ≤ c8 <3.650 ≤ c9 <4.075 ≤ c10. For β diversity: c1 <0.7 ≤ c2 <0.8 ≤ c3 <0.9 ≤ c4 <1.0 ≤ c5 <1.1 ≤ c6 <1.2 ≤ c7 <1.3 ≤ c8 <1.4 ≤ c9 <1.5 ≤ c10. For ϒ diversity: c1 <1.04 ≤ c2 <1.48 ≤ c3 <1.92 ≤ c4 <2.36 ≤ c5 <2.80 ≤ c6 <3.24 ≤ c7 <3.68 ≤ c8 <4.12 ≤ c9 <4.56 ≤ c10
Fig. 7 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 7 Immunolocalization of MSP in E. brevis sperm. a Immature spermatozoon from male. MSP is diffusely distributed in cytoplasm and concentrated in large granules (scale bar 10 µm). b Spermatozoon recovered from male and partially activated by 10-min incubation in sea water. MSP undergoes transformation resulting in appearance of
Fig. 5 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 5 Western blot analysis of MSP in E. brevis. a MSP has unusual mobility in gel and is found as protein with weight 36–38 kDa. Both male and female samples reveal MSP signal, because the latter include inseminated females. α-Tubulin was used as a loading control (approximate weight 55 kDa). b Peptide competition assay confirms reactivity of anti-MSP antibodies with protein band of 36–38 kDa
Fig. 2 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 2 Western blot analysis of MSP in P. redivivus. In adult animals, MSP is detected as double band with approximate weight 15 and 16 kDa. a Both male and female samples reveal MSP signal, because the latter include mated females. α-Tubulin was used as a loading control (approximate weight 55 kDa). b Analysis of young males and females. MSP is not detected in females, because most of them are unmated. Abbreviations: m, males; f, females
Fig. 3 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 3 Schematic representation of P. redivivus spermatozoa based on transmission electron microscopy. a Morphology of immature and mature spermatozoa. Immature spermatozoon is an unpolarized cell with nucleus devoid of nuclear envelope, mitochondria, and membranous organelles. Mature spermatozoon in female reproductive system is a bipolar cell with anterior pseudopodium and posterior main cell body containing chromatin, mitochondria, and membranous organelles that attached to cell membrane and open to the exterior via pores. Reproduced from Zograf (2014) with the permission from copyright holder (Russian Journal of Nematology). b Chain of conjugated mature spermatozoa in female reproductive system. Abbreviations: N, nucleus; mt, mitochondria; mo, membranous organelles; ch, nuclear chromatin; ps, pseudopodium; mcb, mail cell body
Fig. 1 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 1 Phylogeny of nematodes and MSP-based sperm motility. Phylogenetic relationships within phylum Nematoda derived primarily from SSU rDNA sequence data are given according to De Ley and Blaxter (2002). Suborders of the order Rhabditida, in which representatives highly homologous MSPs are found at DNA, RNA, or protein levels, are marked by underlining. Taxa whose species used in this study are marked with asterisks. Orders Trefusi- ida, Isolaimida, Dioctophyma- tida, Muspiceida, Marimermith- ida, and Desmoscolecida are not shown in this tree
Fig. 8 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 8 Putative MSPs those are most similar to peptide antigen. a P. redivivus MSPs aligned with peptide antigen. Protein sequences (Pan_g61.t1, Pan_g6018.t1, Pan_g6424.t1, Pan_g9068.t1, Pan_ g19433.t1, and Pan_g21178.t1) were found by Blast using peptide
Fig. 4 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 4 Immunolocalization of MSP in P. redivivus sperm. a Immature spermatozoa extracted from male. MSP localizes in granules. In some cells, MSP has strongest signals in the periphery (arrowheads) (scale bar 10 µm). b Chain of mature spermatozoa extracted from female.
Data from: Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome
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Phylogenetic analysis of 218 protein sequences that bear sequence similarity to F. prausnitzii FAAH
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Amplicon_sorter: a tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences
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Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf
<p>Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf.</p> <p>Ludt, W.B., Jabado, R.W., Al Hameli, S.M., Freeman, L., Teruyama, G., Chakrabarty, P. & Al Dhaheri, S.S. (2020) Establishing a reference collection and DNA barcoding the coastal fishes of the United Arab Emirates. <em>Journal of the Ocean Science Foundation</em>, 35, 54–64.</p>
Australian long-finned pilot whales (Globicephala melas) emit stereotypical, variable, biphonic, multi-component, and sequenced vocalisations, similar to those recorded in the northern hemisphere
<p>While in the northern hemisphere, many studies have been conducted on the vocal repertoire of long-finned pilot whales (<i>Globicephala melas</i>), no such study has been conducted in the southern hemisphere. Presented here, is the first study on the vocalisations of long-finned pilot whales along the southern coast of mainland Australia. Multiple measures were taken of<b> </b>2 028 vocalisations recorded over five years in several locations. These vocalisations included tonal sounds with and without overtones, sounds of burst-pulse character, graded sounds, biphonations, and calls of multiple components. Vocalisations were further categorised based on spectrographic features into 18 contour classes. Altogether, vocalisations ranged from approximately 200 Hz to 25 kHz in fundamental frequency and from 0.03 s to 2.07 s in duration. These measures compared well with those from northern hemisphere pilot whales. Some call types were almost identical to northern hemisphere vocalisations, even though the geographic ranges of the two populations are far apart. Other call types were unique to Australia. Striking similarities with calls of short-finned pilot whales (<i>Globicephala macrorhynchus</i>) and sometimes sympatric killer whales (<i>Orcinus orca</i>) were also found. Theories for call convergence and divergence are discussed.</p>
Similarity matrix between the core genome sequences
<p>Data table.</p>
Figure 5 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Figure 5 - Relative abundance distribution of fungal leaf-inhabiting endophytes of beech among the five main trophic guilds as revealed by analysis with FUNGuild (Nguyen et al. 2016). A compares the two localities for each trophic guild on the basis of Illumina data B compares the two localities for each trophic guild on the basis of cultivation data.
Figure 4 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Figure 4 - Relative abundance of fungal leaf-inhabiting endophytes of beech among the five main trophic guilds as revealed by analysis with FUNGuild (Nguyen et al. 2016). A compares the two methods for each trophic guild and unassigned data. B displays the trophic guilds and unassigned taxa for Illumina data, C for cultivation data. Abbreviations in [B and C]: U = Unassigned, P = Pathotrophs, PSa = Patho-Saprotrophs, PSy = Patho-Symbiotrophs, Sa = Saprotrophs, Sy = Symbiotrophs
Figure 2 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Figure 2 - . Principal coordinate analysis (PCoA) of fungal leaf-inhabiting endophytes of beech display strongly differing assemblages obtained with Illumina sequencing and cultivation. Both methods revealed differing mycobiomes from valley and from mountain leaves, although these differences were less pronounced for cultivation data. Abbreviations: IM = Illumina data from mountain samples, IV = Illumina data from valley samples, CM = cultivation data from mountain samples, CV = cultivation data from valley samples
Figure 3 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Figure 3 - Abundance distribution of the 20 most abundant orders of fungal leaf-inhabiting endophytes of beech on a logarithmic scale. Three of the five most abundant orders from high-throughput sequencing were also most abundant in cultivation data.
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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.