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.
89
datasets available to search
ShareScore release 0.9.0
Dataset results
89 results for “sequence annotation”
Whole genome sequence and annotation of Penstemon davidsonii
<p><em><span>Penstemon</span></em><span> is the most speciose flowering plant genus endemic to North America. <em>Penstemon</em> species' diverse morphology and adaptation to various environments have made them a valuable model system for studying evolution, but the absence of publicly available reference genomes limits possible research directions. Here we report the first reference genome assembly and annotation for <em>Penstemon</em> <em>davidsonii</em>. Using PacBio long-read sequencing and Hi-C scaffolding technology, we constructed a de novo reference genome of 437,568,744 bases, with a contig N50 of 40 Mb and L50 of 5. The annotation includes 18,199 gene models, and both the genome and transcriptome assembly contain over 95% complete eudicot BUSCOs. This genome assembly will serve as a valuable reference for studying the evolutionary history and genetic diversity of the <em>Penstemon</em> genus.</span></p>
Whole genome sequence and annotation of Penstemon davidsonii
Open the record for dataset details and reuse information.
Amino acid sequences of annotated genes in Pelargonium zonale
Open the record for dataset details and reuse information.
A root-specific NLR network confers resistance to plant parasitic nematodes - genomic sequences and annotations
<p>Sequence and annotation data associated with "A root-specific NLR network confers resistance to plant parasitic nematodes"</p>
Data and scripts for the manuscript of svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
<p>This upload include data and scripts supporting the results described in the manuscript of <em>svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data</em><em>. </em>Detailed description of the contents can be found in README.txt.</p>
Database of 16S sequences from SILVA (r114), filtered, curated and annotated to be used easily by programs of taxonomic assignments
<p>The database used for the taxonomic assignment of reads generally comes from the SILVA database (http://www.arb-silva.de/). The logic behind this database is to use the information from the best one to the worst one. This is why the curated database was splitted in two parts : the [C] sequences for Complete sequences in terms of taxonomy, and the [I] and [E] sequences, for Incomplete and Environmental sequences.</p> <p>Each sequence included into the database must have a specific format summarizing all needed information (example below):<br> >[I]AACY020336309;Archaea(superkingdom);Euryarchaeota(phylum);Thermoplasmata(class);Thermoplasmatales(order);Marine_Group_II(no_rank);;marine_metagenome</p> <p>This sequence is an incomplete one ([I]), with a specific accession number from NCBI or SILVA, or another database (AACY020336309). Then, all taxonomic data is separated using ';' characters, for each considered level (superkingdom, phylum, <br> class, order, family, and genus). The species name is the last one and separated by two ';' characters from the rest of the descriptive line. Finally, the descriptive line must not contain specific characters like spaces. If one or several levels are unknown, this is indicated by 'no_rank'.</p> <p>Another example here for [C] sequences:<br> >[C]AAAK03000010;Bacteria(superkingdom);Firmicutes(phylum);Bacilli(class);Lactobacillales(order);Enterococcaceae(family);Enterococcus(genus);;Enterococcus_faecium_DO<br> This sequence is a complete one ([C]), with a specific accession number from NCBI or SILVA, or another database (AACY020187844). Then, all taxonomic data is separated using ';' characters, for each considered level (superkingdom, phylum, <br> class, order, family, and genus). The species is the last one and separated by two ';' characters from the rest of the descriptive line. Complete sequences must have six levels of information (superkingdom, phylum, class, order, family, and genus). If it is not the case, the sequence will be considered as Incomplete ([I]) (between three and five levels), or Environmental ([E]) (with only the superkingdom and the phylum levels).</p> <p>Another example here for [E] sequences:<br> >[E]U59968;Archaea(superkingdom);Thaumarchaeota(phylum);Soil_Crenarchaeotic_Group(SCG)(no_rank);;uncultured_crenarchaeote<br> This sequence is a environmental one ([E]), with a specific accession number from NCBI or SILVA, or another database (U59968). Then, all taxonomic data is separated using ';' characters, for each considered level (superkingdom, phylum, class, order, family, and genus). The species is the last one and separated by two ';' characters from the rest of the descriptive line. Complete sequences <br> must have six levels of information (superkingdom, phylum, class, order, family, and genus). If it is not the case, the sequence will be considered as Incomplete ([I]) (between three and five levels), or Environmental ([E]) (with only the superkingdom and the phylum levels).</p> <p>More details on the steps defined to clean and define this new database can be available on demand (sebastien.terrat@inra.fr).</p>
Melange (COGs and Pfams) and AntiSMASH (BGCs) annotations of the genome sequence of Lentilitoribacter sp. EG35
<p>Secondary Metabolite Encoding Biosynthetic Gene Cluster (BGC) annotation files from antiSMASH bacterial version 7.1.0 as well as Clusters of Orthologous Groups of proteins (COG) and Protein families (Pfam) annotations from the Melange pipeline (<a href="https://github.com/sandragodinhosilva/melange">https://github.com/sandragodinhosilva/melange</a>) of the genome assembly of <em>Lentilitoribacter </em>sp. strain EG35, isolated from the temperate octocoral <em>Eunicella gazella</em> sampled in the Northeast Atlantic Ocean, Portugal. </p> <p>The data correspond to the genome assembly of EG35 available under the BioProject accession number<a href="https://www.ncbi.nlm.nih.gov/bioproject/1075806"> PRJNA1135483</a>.</p> <p>To interactively view the AntiSMASH results, please download and extract the entire content of the AntiSMASH folder, and open the HTML file named "index".</p> <p><strong>This dataset is part of the following study:</strong></p> <p><strong>Tina Keller-Costa, Selene Madureira, Ana S. Fernandes, Lydia Kozma, Jorge M.S. Gonçalves, Cristina Barroso, Conçeicão Egas, & Rodrigo Costa<sup> </sup>2024. Genome sequence of the marine alphaproteobacterium <em>Lentilitoribacter</em> sp. EG35 isolated from the temperate octocoral <em>Eunicella gazella</em>. Microbiology Resource Announcements. MRA00872-24.</strong></p>
179 high quality metagenome-assembled genomes sequences and annotations
<p>We analyzed seven sediment samples collected adjacent to ferromanganese nodules from the Clarion–Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean. Through deep metagenomic sequencing, assembly, and binning, we reconstructed 179 high quality metagenome-assembled genomes (MAGs). This archive contains these genomes sequences and annotations. </p>
Serratia fonticola EBS19 Whole genome sequence data fasta file annotated
<p>Whole genome sequence data of <em>Serratia fonticola</em> <strong>EBS19 </strong>strain.</p>
Dataset - Functional annotation for protein sequences
<p>These are the input and output files for the functional annotation of protein sequences workflow tests.</p>
Annotation and evolutionary analysis of chemosensory gene sequence data in the Colorado potato beetle, Leptinotarsa decemlineata
Open the record for dataset details and reuse information.
Genome sequence assembly and annotation of MATA and MATB strains of <em>Yarrowia lipolytica</em>
Open the record for dataset details and reuse information.
Database for mi-faser: Functional sequencing read annotation for high precision microbiome analysis
<p><strong>[Database for mi-faser]</strong></p> <p><strong>mi-faser: </strong><em>microbiome - functional annotation of sequencing reads</em></p> <p>A super-fast ( < 20min/10GB of reads ) and accurate ( > 90% precision ) method for annotation of molecular functionality encoded in sequencing read data without the need for assembly or gene finding.</p> <p>Web Service: http://services.bromberglab.org/mifaser/|<br> Repository: https://bitbucket.org/bromberglab/mifaser_base/</p>
Single cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis
<p>Single <span>cell RNA sequencing (scRNAseq) is a powerful technique that continues to expand across various biological applications. However, incomplete 3' UTR annotations can impede single cell analysis resulting in genes that are partially or completely uncounted. Performing scRNAseq with incomplete 3' UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences. We demonstrate that performing single cell isoform sequencing (ScISOr-Seq) in tandem with scRNAseq can rapidly improve 3' UTR annotations. Using threespine stickleback fish (</span><em>Gasterosteus aculeatus</em><span>), we show that gene models resulting from a minimal embryonic ScISOr-Seq dataset retained 26.1% greater scRNAseq reads than gene models from Ensembl alone. Furthermore, pooling our ScISOr-Seq isoforms with a previously published adult bulk Iso-Seq dataset from stickleback, and merging the annotation with the Ensembl gene models, resulted in a marginal improvement (+0.8%) over the ScISOr-Seq only dataset. In addition, isoforms identified by ScISOr-Seq included thousands of new splicing variants. The improved gene models obtained using ScISOr-Seq lead to successful identification of cell types and increased the reads identified of many genes in our scRNAseq stickleback dataset. Our work illuminates ScISOr-Seq as a cost-effective and efficient mechanism to rapidly annotate genomes for scRNAseq.</span></p>
Xcc BrA1 re-sequenced genome contigs, annotation file and Trinitiy De-nove assembled DEG's
<p>Assembled genome contigs of Xcc strain BrA1 (Behlau et al 2017) which was re-sequenced by our lab and used in a copper stress Transcriptome study. A hybrid RNA-seq analysis pipeline was used and the DEG Trinity De-novo assembled transcripts are also included.</p>
Supplementary material 3 from: Abarenkov K, Adams RI, Irinyi L, Agan A, Ambrosio E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra V, Coleine C, Gustafsson C, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M, Svantesson S, Scharn R, Svensson O, Töpel M, Unterseher M, Visagie C, Wurzbacher C, Taylor AFS, Kõljalg U, Schriml L, Nilsson RH (2016) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 16: 1-15. https://doi.org/10.3897/mycokeys.16.10000
Krona chart : Explanation note: Interactive Krona chart for visualizing the taxonomic distribution of annotated BMS sequences down to order level. Sequences classified as Fungi sp. (36.4%) or non-fungal (0.9%) were excluded from this dataset.
Supplementary material 1 from: Abarenkov K, Adams RI, Irinyi L, Agan A, Ambrosio E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra V, Coleine C, Gustafsson C, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M, Svantesson S, Scharn R, Svensson O, Töpel M, Unterseher M, Visagie C, Wurzbacher C, Taylor AFS, Kõljalg U, Schriml L, Nilsson RH (2016) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 16: 1-15. https://doi.org/10.3897/mycokeys.16.10000
Keywords used to identify fungal sequences from the built environment in the INSDC : Explanation note: Keywords used to identify fungal sequences from the built environment in the INSDC.
Supplementary material 2 from: Abarenkov K, Adams RI, Irinyi L, Agan A, Ambrosio E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra V, Coleine C, Gustafsson C, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M, Svantesson S, Scharn R, Svensson O, Töpel M, Unterseher M, Visagie C, Wurzbacher C, Taylor AFS, Kõljalg U, Schriml L, Nilsson RH (2016) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 16: 1-15. https://doi.org/10.3897/mycokeys.16.10000
Annotations made during the workshop : Explanation note: The annotations made during the workshop shown with original INSDC data. For the BMS, we targeted nine MIxS-BE items plus country of collection, host of collection, host association, and a general "Comment" field. For the OMS, we targeted country of collection, host of collection, host association, and a general "Comment" field.
Supplementary material 1 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The sequences renamed during the workshop. The INSDC accession number, the original INSDC name, and the new UNITE name are shown :
Supplementary material 3 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The metadata annotations for the sequences that were found in the same SHs as sequences from the built environment :
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.