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89 results for “sequence annotation”
Timema genome sequences and annotations. Version 8.
<p>Genome sequence (fasta) files and annotation (gff) files for ten <em>Timema </em>species: <em>T. bartmani, T. cristinae, T. poppensis, T. californicum, T. podura, T. tahoe, T. monikensis, T. douglasi, T. shepardi, and T. genevievae.</em><br> <br> Species are abbreviated as follows: Tbi = <em>T. bartmani</em>, Tce = <em>T. cristinae</em>, Tps = <em>T. poppensis</em>, Tcm = <em>T. californicum</em>, Tpa = <em>T. podura</em>, Tte = <em>T. tahoe</em>, Tms = <em>T. monikensis</em>, Tdi = <em>T. douglasi</em>, Tsi = <em>T. shepardi</em>, and Tge = <em>T. genevievae</em><br> </p> <p>For details of assembly and annotation see: <br> <br> Jaron, K. S*., Parker, D. J*., Anselmetti, Y., Tran Van, P. T., Bast, J., Dumas, Z., Figuet, E., François, C. M., Hayward, K., Rossier, V., Simion, P., Robinson-Rechavi, M., Galtier, N., Schwander, T. 2021. Convergent consequences of parthenogenesis on stick insect genomes. bioRxiv. doi: https://doi.org/10.1101/2020.11.20.391540</p> <p> </p> <p><strong>File list:</strong><br> <br> Tbi_b3v08.fasta = T. bartmani genome sequence file<br> Tbi_b3v08.max_arth_b2g_droso_b2g.gff = T. bartmani genome annotation file<br> Tce_b3v08.fasta = T. cristinae genome sequence file<br> Tce_b3v08.max_arth_b2g_droso_b2g.gff = T. cristinae genome annotation file<br> Tcm_b3v08.fasta = T. bartmani genome sequence file<br> Tcm_b3v08.max_arth_b2g_droso_b2g.gff = T. californicum genome annotation file<br> Tdi_b3v08.fasta = T. douglasi genome sequence file<br> Tdi_b3v08.max_arth_b2g_droso_b2g.gff = T. douglasi genome annotation file<br> Tge_b3v08.fasta = T. genevievae genome sequence file<br> Tge_b3v08.max_arth_b2g_droso_b2g.gff = T. genevievae genome annotation file<br> Tms_b3v08.fasta = T. monikensis genome sequence file<br> Tms_b3v08.max_arth_b2g_droso_b2g.gff = T. monikensis genome annotation file<br> Tpa_b3v08.fasta = T. podura genome sequence file<br> Tpa_b3v08.max_arth_b2g_droso_b2g.gff = T. podura genome annotation file<br> Tps_b3v08.fasta = T. poppensis genome sequence file<br> Tps_b3v08.max_arth_b2g_droso_b2g.gff = T. poppensis genome annotation file<br> Tsi_b3v08.fasta = T. shepardi genome sequence file<br> Tsi_b3v08.max_arth_b2g_droso_b2g.gff = T. shepardi genome annotation file<br> Tte_b3v08.fasta = T. tahoe genome sequence file<br> Tte_b3v08.max_arth_b2g_droso_b2g.gff = T. tahoe genome annotation file</p>
Annotation of Phytozome V12 protein plant sequences using the ragp pipeline for hydroxyproline-rich glycoprotein mining
<p>Hydroxyproline aware annotation of hydroxyproline-rich glycoprotein (HRGP) sequences was performed on sequence data from 62 plant proteomes obtained from Phytozome database (<a href="https://phytozome.jgi.doe.gov/pz/portal.html">https://phytozome.jgi.doe.gov/pz/portal.html</a>, version 12) using the ragp R package (<a href="https://github.com/missuse/ragp">https://github.com/missuse/ragp</a>, version 0.3.0.0001). </p> <p>In each archive a single comma separated value table (.csv) is present along with a README.txt file describing the contents of the corresponding .csv file. The archives are:</p> <p>- phytozome_V12.tar.gz - sequences from 62 plant proteomes (phytozome V12) with a total of 2797062 protein sequences.</p> <p>- phytozome_V12_phobius.tar.gz -<strong> </strong> Signal peptide prediction using Phobius (<a href="http://phobius.sbc.su.se/">http://phobius.sbc.su.se/</a>) on sequences present in phytozome_V12.tar.gz.</p> <p>- phytozome_V12_signalp.tar.gz -<strong> </strong> Signal peptide prediction using SignalP 4.1 (<a href="http://www.cbs.dtu.dk/services/SignalP-4.1/">http://www.cbs.dtu.dk/services/SignalP-4.1/</a>) on sequences present in phytozome_V12.tar.gz.</p> <p>- phytozome_V12_targetp.tar.gz - Signal peptide prediction using TargetP 1.1 (<a href="http://www.cbs.dtu.dk/services/TargetP/">http://www.cbs.dtu.dk/services/TargetP/</a>) on sequences present in phytozome_V12.tar.gz.</p> <p>- phytozome_V12_predict_hyp.tar.gz - Probability of proline hydroxylation for each proline from 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1).</p> <p>- phytozome_V12_maab.tar.gz - Motif and amino acid bias (MAAB) classification of hydroxyproline-rich glycoproteins performed on 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1). The number of predicted hydroxyprolines in each sequence is also indicated (based on predictions provided in phytozome_V12_predict_hyp.tar.gz).</p> <p>- phytozome_V12_scan_ag.tar.gz. - Hydroxyproline aware arabinogalactan motif scan performed on 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1). Hydroxyproline predictions are provided in phytozome_V12_predict_hyp.tar.gz. </p> <p>- phytozome_V12_scan_ag_hmmscan.tar.gz - Detection of domains in a subset of protein sequences which were found to contain arabinogalactan motifs (a subset of phytozome_V12_scan_ag.tar.gz).</p> <p>The list of the 62 plant species is provided in phytozome_V12.tar.gz README.txt.</p> <p>For questions contact mdragicevic@ibiss.bg.ac.rs.</p> <p> </p> <p> </p>
Genbank annotation and sequence of the genome of a Rickettsiales symbiont of Reticulomyxa filosa
<p>The genome sequence of a Rickettsiales symbiont was selectively from the genome sequencing reads of its host, Reticulomyxa filosa. Those sequences were obtained from a previous third-party study (doi: 10.1016/j.cub.2013.11.027). The selective assembly procedure was based on GC content and coverage of contigs obtained from the total read sets with SPAdes. Full details are provided in the manuscript file.<br>The obtained symbiont sequence was then annotated with Prokka, and the gbk output file selected.</p><p>This genome was obtained and analysed in the context of a larger genome comparative studies on the Rickettsiales, aimed to investigate the evolutionary patterns within the whole lineage.</p>
Dataset of UAV thermal video sequences with annotations for MOTS benchmarking
<p>Instance segmentation dataset created for the research 'Monitoring Mammalian Herbivores via Convolutional Neural Networks implemented on Thermal UAV imagery'. It comprises 959 frames, 20.647 masks, and 239 tracks, and consists of 7 video sequences depicting aerial thermal imagery of cattle collected with a UAV (Parrot ANAFI Thermal) in two outdoor farms in the Netherlands. Data were acquired at three temperatures (10ºC, 19ºC, and 26.5ºC), under sunny and overcast weather conditions, at various angles of inclination (including nadir), and at heights ranging between 8-28 meters. Ground truth was labeled manually with the Computer Vision Annotation Tool <em>CVAT</em>.</p>
MGBC-26640: nucleotide sequences for gene annotations
<p>Nucleotide sequences of annotated genes from the 26,640 high-quality, non-redundant genomes of the MGBC.</p>
Training data for 'Functional annotation of protein sequences' tutorial (Galaxy Training Material)
<p>The data provided here are part of a Galaxy Training Network tutorial for functional annotation of protein sequences.</p>
Sei whole-genome sequence class annotations
<p>Sei sequence class whole-genome annotations are available in the following files:</p> <ul> <li> <p>sorted.hg38.tiling.bed.ipca_randomized_300.labels.merged.bed - The sorted, merged sequence class assignments from Louvain community clustering of the 30 million sequences, uniformly tiling the whole human genome. The fourth column is the sequence class number, with any sequence classes numbering 40-61 excluded from our analyses in the publication. Sequence classes 0-39 can be mapped to the following labels: <a href="https://github.com/FunctionLab/sei-framework/blob/main/model/seqclass.names">https://github.com/FunctionLab/sei-framework/blob/main/model/seqclass.names</a></p> </li> <li> <p>sorted.hg19.tiling.bed.ipca_randomized_300.labels.merged.bed - lifted over version of the hg38 BED file.</p> </li> </ul>
Genome annotations of Drosophila melanogaster and Drosophila simulans wild-type strains from long read sequencing assemblies
<p>Genome assemblies were performed for eight wild-type strains of Drosophila melanogaster and Drosophila simulans from Oxford Nanopore long read sequencing (please refer to Mohamed et al. Cells 2020 (doi:10.3390/cells9081776)). Assemblies were deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB50024 (<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEBxxxx">https://www.ebi.ac.uk/ena/browser/view/</a>PRJEB50024).</p> <p>Transposable Element annotations: we used RepeatMasker 4.1.0 (<a href="http://repeatmasker.org/">http://repeatmasker.org/</a>) -species Drosophila, followed by OneCodeToFindThemAll (Bailly-Bechet et al. 2014) with default parameters.</p> <p>Gene annotations: We retrieved gtf files from FlyBase : <a>ftp.flybase.net/genomes/D</a><a>rosophila_melanogaster/dmel_r6,46_FB2022_03/gft/dmel-all-r6.46.gtf.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/gtf/dsim-all-</a><a>r2,02.gtf.gz</a>. The corresponding fasta files were also downloaded from FlyBase: <a>ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/</a><a>fasta</a><a>/dmel-all-</a><a>chromosome-</a><a>r6.46.</a><a>fasta</a><a>.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/</a><a>fasta</a><a>/dsim-all-</a><a>chromosome-</a><a>r2,02.</a><a>fasta</a><a>.gz</a>. We used Liftoff (Shumate and Salzberg, 2020) to lift over gene annotations from the references to our genome assemblies. We used -flank 0.2 and only kept the “gene” and “exon” terms.</p>
Microscopy image sequences and annotated kymographs of laser ablation experiments in Drosophila embryos
<p><strong>Content</strong></p> <p>This dataset contains 15 2D time-lapse fluorescence microscopy image sequences recorded with confocal laser-scanning microscopy. Each movie shows an epithelial tissue laser nanoablation experiment conducted in a Drosophila embryo.</p> <p>For each sequence, the dataset contains kymographs (one-dimensional space-time plots) of a supracellular cable that is cut during the ablation, and manually created tracks of visible features, such as the resulting cut ends. These tracks allow to estimate, for instance, recoil velocities of the cut tissue and may be used to evaluate automated methods for estimating said velocities.</p> <p>This dataset is used in the manuscript to evaluate various variational approaches for joint motion estimation and source identification:</p> <p>L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schönlieb, and J. Étienne. Joint Motion Estimation and Source Identification using Convective Regularisation with an Application to the Analysis of Laser Nanoablations. 2019.</p> <p><strong>Description</strong></p> <p>The movies depict a square region of approximately <span class="math-tex">\(42.2 \times 42.2 \, \mathrm{\mu m}^{2}\)</span> at a spatial resolution of <span class="math-tex">\(250 \times 250\)</span> pixels. A typical sequence contains between 60 and 100 frames. They temporal interval between recorded frames was <span class="math-tex">\(727.67 \, \mathrm{ms}\)</span>.</p> <p>Each sequence features cell membranes labelled with E-cadherin:GFP and shows a single plasma-induced laser nanoablation. The destructed tissue region is roughly of <span class="math-tex">\(2 \, \mathrm{\mu m}\)</span> length. This ablation is expected to have a width of the order of the size of one pixel. During the ablation the acquisition is paused, resulting in a black image.</p> <p>For the used microscopy techniques and for the preparation of flies, as well as for the details of the laser ablation method, see the paper:</p> <p>E. Scarpa, C. Finet, G. B. Blanchard, and B. Sanson. Actomyosin-driven tension at compartmental boundaries orients cell division independently of cell geometry In Vivo. Dev. Cell, 47(6):727–740.e6, December 2018. URL: <a href="https://doi.org/10.1016/j.devcel.2018.10.029">https://doi.org/10.1016/j.devcel.2018.10.029</a></p> <p>The kymographs and the manually created annotations (tracks) of features were created using Fiji (<a href="https://fiji.sc/">https://fiji.sc/</a>).</p> <p><strong>Content</strong></p> <p>The dataset contains 15 sequences placed in the following folder structure:</p> <ul> <li>SqAX3_SqhGFP42_GAP43_TM6B <ul> <li>190216E4PSB1</li> <li>190216E5PSB1</li> <li>190216E5PSB2</li> <li>190216E6PSB1</li> <li>190216E8PSB1</li> <li>E2PSB1</li> <li>E5PSB2</li> <li>E8PSB1</li> <li>PSB1E1</li> <li>PSB4</li> </ul> </li> <li>SqhGFP40 <ul> <li>e1_PSB8</li> <li>e3_PSB9</li> <li>e3_PSB10</li> <li>e4_PSB11</li> <li>e4_PSB12</li> </ul> </li> </ul> <p>Each folder contains:</p> <ul> <li>The sequence itself in TIF format, e.g. "190216E4PSB1PMT - PMT [560-] _C1.ome.tif".</li> <li>A file "reslice.roi" that indicates the location/direction of the cut supracellular cable.</li> <li>3 different kymographs for each sequence obtained by taking avg/max/sum projections in Fiji orthogonal to the line specified in "reslice.roi", e.g. <ul> <li>"AVG_Reslice of 190216E4PSB1PMT.tif",</li> <li>"MAX_Reslice of 190216E4PSB1PMT.tif",</li> <li>"SUM_Reslice of 190216E4PSB1PMT.tif".</li> </ul> </li> <li>Text files that state the time/space coordinates of manually tracked features in the kymographs, e.g. <ul> <li>"cutend_L.txt" (coordinates of the left cut end after the ablation),</li> <li>"cutend_R.txt" (coordiantes of the right cut end),</li> <li>"feat_X.txt" (coordinates of additional features, where X is a number and L or R).</li> </ul> </li> <li>A ZIP file "manual_ROIs.zip" that contains all the coordinates of tracked features of the kymograph in ROI format (e.g. "cutend_L.roi").</li> </ul> <p><strong>Usage</strong></p> <p>The sequences, kymographs, and the tracks can be viewed using, for example, Fiji.</p> <p>For the automated analysis, see the Python code that accompanies the manuscript above. It is available at https://dx.doi.org/XXX</p> <p><strong>License information</strong></p> <p>This dataset is released under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. See <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NA-SC 4.0</a>.</p> <p><strong>How to cite this dataset</strong></p> <p>If you use this dataset in an academic publication, please consider citing the paper:</p> <p>L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schönlieb, and J. Étienne. Joint Motion Estimation and Source Identification using Convective Regularisation with an Application to the Analysis of Laser Nanoablations. 2019.</p> <p>To cite solely the dataset, please use:</p> <p>L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schönlieb, and J. Étienne. (2019). Microscopy image sequences and annotated kymographs of laser ablation experiments in Drosophila embryos [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.3257654">http://doi.org/10.5281/zenodo.3257654</a></p>
The Caedibacter taeniospiralis genome sequence and annotation
<p>Interest in host-symbiont interactions is continuously increasing, not only due to the relevance and<br> prevalence of microbiomes. Started with the detection and description of novel symbionts, attention<br> moves to the molecular consequences and innovations of symbioses. However, molecular analysis requires<br> genome data which is dicult to obtain from obligate intracellular and uncultivated bacteria.We describe<br> here the Caedibacter taeniospiralis genome and transcriptome, identified by DNA and RNA Dual-Seq<br> of infected paramecia.</p> <p>Data inlcudes a genome FASTA file, annotations of genes and operons in gff format, and the compelte annotation in Geneious format.</p>
Fig. 5 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 5. Phylogenetic tree based on analysis of mitochondrial COI sequences of the Sarcocystidae including the new Sarcocystis sp. examined in this study (black symbols). Other taxa of the Apicomplexa served as root. Evolutionary history was inferred by the Maximum Likelihood (ML) method based on the TamuraNei model, whereby 619 positions were included in the final data set. All positions with less than 95% site coverage were eliminated; that is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. Bootstrap percentages (1000 iterations) are shown next to branches. COI sequences E357-13 and E120-13 (not shown in the tree) are available at GenBank (MN732561 and MN732562, respectively).
Fig. 2 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 2. Ultrastructure of S. scandentiborneensis sp. nov. Note, due to ethanol-fixation some ultrastructural details are poorly resolved (e.g. membranes). A) Longitudinal section through the same sample as in Fig. 1C, showing a gross view of the sarcocyst and its villous protrusions (VP) that are sectioned in different orientations. The inset shows a cross section through various VP that reveals the arrangement of microtubules in their inner core; while in this case 16 microtubules are visible (asterisks), sections through more apical portions of the VP showed lower numbers. B) Longitudinal section through the fingerlike VPs that appear to be anchored in the ground substance (arrow) by microtubules (asterisks) that extend into each protrusion; note the electron-dense, U-shaped structure at each tip of the protrusions (arrowheads) and the apparently serrated surface of the VP (flat arrowheads). The inset shows a higher magnification of the apical part of a single VP with the typical U-shaped apex (asterisk), which appears to be connected with the host cell through an electronlucent contact zone (white arrowheads); interestingly, the protrusion appears fenestrated (also visible in the main image) possessing thorn-like structures (black arrows; the white arrow indicates a crosssectional view) that could be responsible for the serration visible at lower magnification. CZ, cystozoites; HC, host cell; VP, villous protrusion.
Fig. 1 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 1. Light microscopy of Sarcocystis scandentiborneensis sp. nov. A and B, Haematoxylin & Eosinstained histological sections of striated musculature; C and D, Richardson's dye-stained 1.0 μm thin sections of sarcocysts. A) Tissue section of laryngeal muscle with various sarcocysts in cross section (asterisks), indicating a relatively high density of cysts in this part of musculature. B) Longitudinal section through a sarcocyst, showing a cigar-shaped appearance; however, isolated native sarcocysts, which were not available, may look different. C) Part of a longitudinal section through the tip of a sarcocyst, note the very thin ground substance (arrows) and the fine septae extending into the interior of the cyst (arrowheads); cystozoites (CZ) were loosely scattered within chambers while metrocytes were rarely seen, indicating maturity of the cyst; bars indicate the variable thickness of the cyst wall: the wall was thinner in regions where the villous protrusions were bent (right bar); note that the intense staining at the interface between host cell (HC) and parasite is part of the host cell. D) Cross-section through a sarcocyst showing cystozoites and the cyst wall (bar) including its thin ground substance (arrows).
Fig. 4 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 4. Mapping (to the Toxoplasma gondii reference molecule M97703) of frequencies (%) of base pair changes observed in sequence comparisons of nu clear 18S rDNA within the new Sarcocystis sp. from treeshrews (intraspecific variation: isolates E364–13 versus E357–13) and between the new species and Sarcocystis zuoi and/or S. clethrionomyelaphis (interspecific variation: E364–13 versus S. zuoi/clethrionomyelaphis). Results were combined for the two latter species to simplify the graph. Here, 87.2% of 2118 alignment positions showed moderate to high levels of consistency, while sections of ambiguous alignment did not relate to the species under investigation. Due to gaps in the alignment, not all of the observed nt changes could be mapped to a homologous position of the reference molecule (i.e., 7 out of 24 bp changes in intraspecific comparison; 33 out of 74 bp changes in interspecific comparison), in which case the position of each nt relative to the helix was inferred from neighboring nt for which such position was known. Gaps were mainly due to insertions in helices V2, V4, and V9 rendering E357-13/E364-13 longer than the sequence of T. gondii. The percentage of parsimony-informative (pi) bp changes per helix is shown for helices V1, V2, V4, V7, and V9 above each column. Also shown is the ratio of transitions versus transversions (Ti/Tv) for selected helices.
Accurate annotation of protein coding sequences with IDTAXA - Training Data
<p>Training data used to test IDTAXA, HMMER, and BLAST performance of classification of amino acid and nucleotide sequences.</p>
Accurate annotation of protein coding sequences with IDTAXA - classification results
<p>Raw classification results generated by IDTAXA, BLAST, and HMMER on a training set scraped from KEGG of > 1.5M sequences. HMMER and BLAST results are also converted into IDTAXA like objects for ease of comparison.</p>
Genome sequences and gene annotations for two Ophryocystis lineages
<p>Assembly, annotation, and gene sequences for the <em>Ophryocystis </em>lineages sequenced in "Genome sequence of <em>Ophryocystis elektroscirrha</em>, an apicomplexan parasite of monarch butterflies: cryptic diversity and response to host-sequestered plant chemicals." Each of the two lineages has three associated files: a genome sequence file (.fa), an annotation in .gff3 format, and gene sequences in .fna format. Sequences generated for <em>Ophryocystis elektroscirrha </em>come from direct DNA extraction and sequencing effort and are hosted elsewhere on NCBI as well. The other lineage, prefixed Ophryocystis-elektroscirrha_like, was bioinformatically extracted from the genome of an infected host. As such, we are less confident in its completeness and it is not archived elsewhere. </p>
Supplemental material of "An annotated whole-genome multilocus sequence typing schema for scalable high resolution typing of Streptococcus pyogenes"
<p>This supplemental material includes the genome assemblies, associated metadata and analysis results for five datasets used to define a publicly available annotated wgMLST schema for <em>S. pyogenes</em> and to evaluate its suitability for high resolution typing. A brief description for each file in the dataset is available in the included README file. Raw sequencing data and sample metadata for the 265 isolates included in Dataset1 have been deposited in the European Nucleotide Archive (ENA) under Project <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB49967?show=reads">PRJEB49967</a>.</p> <p>The wgMLST schema was created with <a href="https://github.com/B-UMMI/chewBBACA">chewBBACA</a> and is publicly available at <a href="https://chewbbaca.online/species/1/schemas/1">chewie-NS</a>, where a more detailed description of schema creation, annotation and curation can be found.</p>
Whole genome sequence and annotation dataset of rare actinobacteria, Barrientosiimonas humi gen. nov., sp. nov. 39T from Antarctica
<p>The present data files are the source files of the annotation output from the whole genome sequencing of rare actinobacteria, <em>Barrientosiimonas humi gen. nov., sp. nov.</em> 39<sup>T</sup> from Antarctica.</p> <p>The dataset of the whole-genome sequence of <em>B. humi</em> had been deposited in European Nucleotide Archive (ENA) repository under the accession number PRJEB44986 / ERP129097, direct URL to data:<strong> </strong><a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB44986">https://www.ebi.ac.uk/ena/browser/view/PRJEB44986</a></p>
Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation
<p>The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikatis. The detailed description of the datafiles and scripts is provided in the accompanying README.rtf file.</p>
ScienceDex guides
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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.