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.
19,342
datasets available to search
ShareScore release 0.9.0
Dataset results
19,342 results for “sequence”
Fig. 3. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with concatenated ITS2 and 28S DNA sequences from 41 in A new genus and three new species of mangrove slugs from the Indo-West Pacific (Mollusca: Gastropoda: Euthyneura: Onchidiidae)
Fig. 3. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with concatenated ITS2 and 28S DNA sequences from 41 individuals (including 7 outgroups). Numbers by the branches are the bootstrap values (only numbers> 50% are indicated). Numbers for each individual correspond to unique identifiers for DNA extraction. All sequences for specimens of Paromoionchis gen. nov. are new. Information on specimens can be found in the lists of material examined and in Table 1. Letters A and B correspond to clades referred to in the text. The color used for each (mitochondrial) unit is the same as that used in Figs 1–2 and 4–6.
Evolution models of helium white dwarf-main-sequence star merger remnants: the mass distribution of single low-mass white dwarfs
<p>Inlists and data for "<a href="https://ui.adsabs.harvard.edu/#abs/2018MNRAS.474..427Z/abstract">Evolution models of helium white dwarf-main-sequence star merger remnants: the mass distribution of single low-mass white dwarfs</a>"</p>
The stability of massive main-sequence stars as a function of metallicity
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2012MNRAS.423.3397S">The stability of massive main-sequence stars as a function of metallicity</a></p>
The observational signatures of convectively excited gravity modes in main-sequence stars
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2013MNRAS.430.1736S">The observational signatures of convectively excited gravity modes in main-sequence stars</a></p>
Mass loss in main-sequence B stars
<p>MESA run_star_extras associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2014A&A...564A..70K">Krtička (2014)</a>. MESA version 7624.</p> <p>Publication DOI: <a href="https://doi.org/10.1051/0004-6361/201321980">10.1051/0004-6361/201321980</a></p>
Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/#abs/2018A&A...615A..78G/abstract">Götberg et al. (2018)</a>. MESA version 8118.</p> <p>Publication DOI: <a href="https://doi.org/10.1051/0004-6361/201732274">10.1051/0004-6361/201732274</a></p>
New full evolutionary sequences of H- and He-atmosphere massive white dwarf stars using MESA
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2018MNRAS.480.1547L">New full evolutionary sequences of H- and He-atmosphere massive white dwarf stars using MESA</a></p>
Discovery of tandem and interspersed segmental duplications using high throughput sequencing
<p>We developed novel algorithms to accurately characterize tandem, direct and inverted interspersed segmental duplications using short read whole genome sequencing data sets. We integrated these methods to our TARDIS tool, which is now capable of detecting various types of SVs using multiple sequence signatures such as read pair, read depth and split read. We evaluated the prediction performance of our algorithms through several experiments using both simulated and real data sets. In the simulation experiments, using a 30x coverage TARDIS achieved 96% sensitivity with only 4% false discovery rate. For experiments that involve real data, we used two haploid genomes (CHM1 and CHM13) and one human genome (NA12878) from the Illumina Platinum Genomes set. Comparison of our results with orthogonal PacBio call sets from the same genomes revealed higher accuracy for TARDIS than state of the art methods. Furthermore, we showed a surprisingly low false discovery rate of our approach for discovery of tandem, direct and inverted interspersed segmental duplications prediction on CHM1 (less than 5\% for the top 50 predictions). </p>
Sequencing data: Fungi, fire and insects: Protea infructescences as reservoirs for fungal biodiversity in fire-prone environments
<p>This is the dataset for a submitted manuscript entitled "Fungi, fire and insects: <em>Protea</em> infructescences as reservoirs for fungal biodiversity in fire-prone environments".</p> <p>The upload contains all forward and reverse paired end .fastq files. The files are already demultiplexed. The metadata.xlsx file contains sample information, gps coordinates, etc.</p> <p> </p>
Nanopore sequence analysis - Galaxy Training Material
<p>Twelve MDR plasmids harboring samples were prepared according to the MinION library construction protocols, followed by library sequencing. After 8 hours of sequencing run, a total of 287 725 reads ranging from dozens to tens of thousands of bases in length were obtained, covering a total of 493 Mbp. The raw data were subjected to several stages of processing, including basecalling, de-multiplexing, fasta sequence extraction. For this tutorial one out of the twelve samples is chosen as example.</p> <p>This dataset is extracted of a project studying the Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data (<a href="https://doi.org/10.1093/gigascience/gix132">https://doi.org/10.1093/gigascience/gix132</a>)</p>
Data for: Beyond signal quality: The value of unmaintained pH, dissolved oxygen, and oxidation-reduction potential sensors for remote performance monitoring of on-site sequencing batch reactors
<p>Sensor maintenance is time-consuming and is a bottleneck for monitoring on-site wastewater treatment systems. Hence, we compare maintained and unmaintained sensors to monitor the biological performance of a small-scale sequencing batch reactor (SBR). The sensor types are ion-selective pH, optical dissolved oxygen (DO), and oxidation-reduction potential (ORP) with platinum electrode. We created soft sensors using engineered features: ammonium valley for pH, oxidation ramp for DO, and nitrite ramp for the ORP. Four soft sensors based on unmaintained pH sensors correctly identified the completion of the ammonium oxidation (89 to 91 out of 107 cycles), about as many times as soft sensors based on a maintained pH sensor (91 out of 107 cycles). In contrast, the DO soft sensor using data from a maintained sensor showed slightly better (89 out of 96 cycles) detection performance than that using data from two unmaintained sensors (77, respectively 82 out of 96 correct). Furthermore, the DO soft sensor using maintained data is much less sensitive to the optimisation of cut-off frequency and slope tolerance than the soft sensor using unmaintained data. The nitrite ramp provided no useful information on the state of nitrite oxidation, so no comparison of maintained and unmaintained ORP sensors was possible in this case. We identified two hurdles when designing soft sensors for unmaintained sensors: i) Sensors' type- and design-specific deterioration affects performance. ii) Feature engineering for soft sensors is sensor type specific, and the outcome is strongly influenced by operational parameters such as the aeration rate. In summary, the results with the provided soft sensors show that frequent sensor maintenance is not necessarily needed to monitor the performance of SBRs. Without sensor maintenance monitoring smalls-scale SBRs becomes practicable, which could improve the reliability of unstaffed on-site treatment systems substantially.</p>
Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii (nucleotide alignment dataset)
<p>This dataset includes the nucleotide alignment of eight Toxoplasma gondii genome loci (Sag1 / Chromossome VIII, Gra6 / Chromossome X, PK1 / Chromossome VI, Sag3 / Chromossome XII, L363 / Chromossome VIIb, CB21-4 / Chromossome III, M102 / Chromossome VIIa, Sag2 / Chromossome VIII). Each alignment includes sequences from T. gondii reference strains (retrieved from ToxoDB) as well as sequences from multiple clinical strains (obtained by Sanger / Next-generation sequencing) of the collection of the National Reference Laboratory of Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Portugal. </p>
Aligned DNA sequence matrixes for the study of the divergent times of phytoplasmas
<p>Sequence alignments of 16S rRNA and methionine aminopeptidase (map) are provided in FASTA files “Cao_et_al_16S.fas” and “Cao_et_al_map.fas”, respectively. Detailed information of the data matrixes is as follows:</p> <p> </p> <p>File name: Cao_et_al_16S.fas</p> <p>Number of taxa: 220</p> <p>Number of characters: 1655</p> <p>Gap: -</p> <p> </p> <p>File name: Cao_et_al_map.fas</p> <p>Number of taxa: 83</p> <p>Number of characters: 564</p> <p>Gap: -</p>
Aligned DNA sequence matrixes for the study of the divergent times of phytoplasmas
<p>Sequence alignments of 16S rRNA and methionine aminopeptidase (map) are provided in FASTA files “Cao_et_al_16S.fas” and “Cao_et_al_map.fas”, respectively. Detailed information of the data matrixes is as follows:</p> <p> </p> <p>File name: Cao_et_al_16S.fas</p> <p>Number of taxa: 220</p> <p>Number of characters: 1655</p> <p>Gap: -</p> <p> </p> <p>File name: Cao_et_al_map.fas</p> <p>Number of taxa: 83</p> <p>Number of characters: 564</p> <p>Gap: -</p>
Sanger sequencing of F1 mice from Y647S founder
<p>Sanger sequencing from genomic DNA</p> <p>from two F1 pups of WTB6M crossed to founder 258F3</p> <p>Demonstrates germline transmission of mutant allele</p> <p>7 heterozygotes and 7 wildtype littermates will be shipped from NIH to U of T in September</p>
Data file with manuscript titled 'A Structurally Validated Sequence Alignment of 497 Human Protein Kinase Domains'
<p>The files used in different analysis reported in the manuscript titled - 'A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains' are shared at two locations. Following is a brief description of these files.</p> <p>Location - https://github.com/DunbrackLab/Kinases<br> 1. HMM profile files - HMM files for each of the nine groups computed separately labeled as Groupname.hmm, like AGC.hmm<br> 2. HMM profile file - HMM file computed from the full alignment including all the sequences - Human-PK.hmm<br> 3. Score files - HMM scores of each kinase sequence against all the groupwise HMMs both for iteration1 (HMM-iter1-scores-tables.txt) and iteration2 (HMM-iter1-scores-tables.txt)<br> 4. Jalview session file - Kinase alignment with sequences colored by secondary structure information from PDB file if the structure is known; or predicted secondary structure if the experimental structure is not known. The file could be opened in Jalview - kinases-PDB-SSPred.jvp</p> <p>Location - https://zenodo.org/record/3445533<br> 1. The file contains list of residue pairs aligned in pairwise structural alignments of 272 human protein kinases which were used as a benchmark in the study. The alignments were created by FATCAT and optimized by SE program.</p>
Intergenic sequences of Solenopsis invicta
<p>Intergenic sequences created as part of the Solenopsis ATLAS project.</p>
Genus level DNA sequence data for three genes (matK, rbcL, trnH-psbA) for the paper: A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability
<p>This data file contains the consensus DNA sequences in fasta format, of 64 tree genera found in Mediterranean Europe, following the checklist of Médail et al. (2019). </p> <p>The data are used in a manuscript submitted for publication to Botany Letters and currently under revision. The manuscript is entitled: "<em>A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability</em>". Its authors are: Marwan Cheikh Albassatneh, Marcial Escudero, Loic Ponge<sup>*</sup>, Anne-Christine Monnet, Juan Arroyo, Toni Nikolic, Gianluigi Bacchetta, Francesca Bagnoli, Panayotis Dimopoulos, Agathe Leriche, Frédéric Médail, Anne Roig, Ilaria Spanu, Giovanni Giuseppe Vendramin, Arndt Hampe, Bruno Fady.</p>
The miRBase release 22 reference files: stem-loop sequences (hairpins) and mature miRNA sequences
<pre>The miRBase Sequence Database -- Release 22 ------------------------------------------- The miRBase database provides a searchable online repository for published microRNA sequences and associated annotation. miRBase also provides a gene naming and nomenclature function in the miRBase Registry. Release 22 of the database contains 38589 entries representing hairpin precursor miRNAs, expressing 48885 mature miRNA products, in 271 species. The data are freely available to all through the web interface at http://www.mirbase.org/ and in flatfile form from ftp://mirbase.org/pub/mirbase/. </pre>
Human sequence alignment data set used for analysis of SPDI algorithm and tools
<p>Collection of alignment segments produced on October 30, 2019. The ADS currently consists of over 2,680,000 pairwise alignment segments generated from over 350,000 distinct input sequences. </p> <ul> <li> <p>Old assembly to current Genome Reference Consortium (GRC) <a href="http://f1000.com/work/citation?ids=111899&pre=&suf=&sa=0">(Church et al., 2011)</a> primary assemblies (e.g. GRCh36(hg18) or GRCh37(hg19) with GRCh38(hg38))</p> </li> </ul> <ul> <li> <p>Patches, alternative loci, or pseudoautosomal regions (PAR) to GRC primary assembly</p> </li> <li> <p>RefSeq <a href="http://f1000.com/work/citation?ids=2599029&pre=&suf=&sa=0">(O’Leary et al., 2016)</a> and select GenBank <a href="http://f1000.com/work/citation?ids=6183037&pre=&suf=&sa=0">(Benson et al., 2018)</a> transcripts to selected RefSeq genomic regions, also known as RefSeqGene (NG), a member of the Locus Reference Genome (LRG) collaboration <a href="http://f1000.com/work/citation?ids=3225699&pre=&suf=&sa=0">(Dalgleish et al., 2010)</a>.</p> </li> <li> <p>Current RefSeq transcripts (NM/NR/XM/XR) and RefSeq genomic regions (NG) to the latest Assembly</p> </li> <li> <p>Previous versions of NG and RefSeq transcripts (NM/NR) to GRC primary assembly</p> </li> </ul>
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.