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1,199 results for “Alignement”
DeepMSA2 alignments used by Zhang group in CASP14
<p>Supporting data for</p> <p>Wei Zheng, Yang Li, Chengxin Zhang, Xiaogen Zhou, Robin Pearce, Eric W Bell, Xiaoqiang Huang, Yang Zhang<br> Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14.<br> Proteins: Structure, Function, and Bioinformatics, 89: 1734-1751 (2021).<br> <br> Yang Li, Chengxin Zhang, Wei Zheng, Xiaogen Zhou, Eric W Bell, Dong‐Jun Yu, Yang Zhang<br> Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14.<br> Proteins: Structure, Function, and Bioinformatics, 89: 1911-1921 (2021).</p>
Aminoacyl-tRNA synthetase gene alignments from multiple Sileneae species generated from full-length transcripts using Iso-Seq and raw microscopy image files
<p>Trimmed and untrimmed alignments for the final aminoacyl-tRNA synthetases in <em>Sileneae </em>species and <em>Arabidopsis thaliana. W</em>e investigated the evolution of subcellular localization of aaRS enzymes in five different species from the plant lineage <em>Sileneae</em> that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts with single-molecule sequencing technology (PacBio Iso-Seq) and searching genome sequences, we found instances of predicted retargeting of an ancestrally cytosolic aaRS to the mitochondrion as well as scenarios where enzyme localization does not appear to change despite functional tRNA replacement.</p> <p>Nikon .nd2 raw microscopy files for the transient expression and imaging of predicted transit peptides and colocalization assays in <em>N. benthamiana</em> epithelial cells. The amino acid sequence plus 10 upstream amino acids of the protein body were fused to GFP and co-transfected with an eqFP611-tagged transit peptide from a known mitochondrially localized protein (isovaleryl-CoA dehydrogenase).</p>
Sergestidae shrimp family single- and multi-gene alignments and tree files
<p>Deep-sea shrimp belonging to the family Sergestidae provide a unique system for studying the evolution of bioluminescence. Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores, non-lensed photophores, or internal organs of Pesta. This morphological diversity across Sergestidae has resulted in recent major taxonomic revisions, dividing the two major genera (<em>Sergia </em>and<em> Sergestes</em>) into 15. Here, we capitalize on molecular data to construct an updated genus-level phylogeny of sergestid shrimp. DNA was successfully extracted from approximately 87 individuals belonging to 13 of the 15 newly proposed genera. We implemented a "genome skimming" approach, allowing us to capture mitochondrial genomic data across 19 Sergestidae species. Additional individuals have been incorporated into the phylogeny through Sanger sequencing of both nuclear (H3, NAK) and mitochondrial (16S and COI) genes. The resulting molecular phylogeny is compared with previous morphological trees with specific attention to genus-level relationships. The -<em>sergestes</em> group was rendered non-monophyletic, and the -<em>sergia</em> group was recovered as monophyletic. Ancestral state reconstructions of light organ type indicate the organs of Pesta is the ancestral state for the family. Non-lensed photophores evolved once across the -<em>sergia</em> group, but were later lost in the deepest living genus, <em>Sergia</em>. Lensed photophores also evolved once within the genera <em>Prehensilosergia</em>, <em>Lucensosersgia</em>, and <em>Challengerosergia</em>. Our findings identify preliminary patterns across light organ type and species' depth distributions, however future research that incorporates finer-scale depth data and more species is needed to confirm our findings. </p>
Core SNP multiple alignments composed by L. garvieae, L. lactis, Streptococcus and Enterococcus strains.
<p>Core SNP multiple alignments composed by L. garvieae, L. lactis, Streptococcus and Enterococcus strains.</p>
Aligned DNA sequences of Vanilla
<p><strong><span>Premise</span></strong></p> <p><span>Although vanilla is one of the best-known spices, there is a limited understanding of its biology and genetics within Mexico, where its cultivation originated and where phenotypic variability is high. This study aims to augment our understanding of vanilla's genetic resources by assessing species delimitation and genetic, geographic, and climatic variability within Mexican cultivated vanilla. </span></p> <p><strong><span>Methods</span></strong></p> <p><span>Nuclear and plastid DNA sequence data from 58 Mexican samples collected from three regions and 133 <em>ex-situ</em> accessions were used to assess species monophyly using phylogenetic analyses and genetic distances. Intra-specific genetic variation was summarized through the identification of haplotypes. Within the primarily cultivated species, <em>V. planifolia</em>, haplotype relationships were further verified using plastome and rRNA gene sequences. Climatic niche and haplotype composition were assessed across the landscape.</span></p> <p><strong><span>Key Results</span></strong></p> <p><span>Three species (<em>Vanilla planifolia</em>, <em>V. pompona</em>, and <em>V. insignis</em>) and 13 haplotypes were identified among Mexican vanilla. Within <em>V. planifolia</em> haplotypes, hard phylogenetic incongruences between plastid and nuclear sequences suggest past hybridization events. Eight haplotypes exclusively consisted of Mexican samples. The dominant <em>V. planifolia</em> haplotype occurred throughout all three regions as well as outside of its country of origin. Haplotype richness was found to be highest in regions around Papantla and La Chinantla.</span></p> <p><strong><span>Conclusions</span></strong></p> <p><span>Long histories of regional cultivation support the consideration of endemic haplotypes as landraces shaped by adaptation to local conditions and/or hybridization. Results may aid further genomic investigations of vanilla's genetic resources and ultimately support the preservation of genetic diversity within the economically important crop.</span></p>
Sample graphs and sequences for testing sequence-to-graph alignment
<p>File descriptions:</p> <ul> <li>MHC-61.agc: 61 complete MHC sequences, including GRCh38, CHM13 and 59 haplotypes extracted from <a href="https://github.com/human-pangenomics/HPP_Year1_Assemblies">HPRC year-1 assemblies</a>. Use <a href="https://github.com/refresh-bio/agc">AGC</a> to extract individual haplotype sequences.</li> <li>MHC-57.gfa.gz: sequence graph constructed by <a href="https://github.com/lh3/minigraph">minigraph</a>-0.18, excluding sample HG002 and HG005</li> <li>C4-96.agc: 96 complete C4 sequences obtained from HPRC</li> <li>C4-90.gfa.gz: sequence graph extracted from the <a href="https://doi.org/10.5281/zenodo.6499594">full HPRC year-1 minigraph graph (v0.17)</a> around the C4A/C4B genes. The graph takes GRCh38 as the reference and excludes sample HG002, HG005 and NA19240.</li> </ul>
Queries and graphs for sequence to graph alignment method evaluation
<p>The tar contains two directories for queries and graphs used to evaluate the sequence to graph alignment methods. </p>
Alignments of chloroplast noncoding regions for context-dependency analysis
<p>Substitutions between closely related noncoding chloroplast DNA sequences are studied with respect to the composition of the three bases on each side of the substitution, that is the hexanucleotide context. There is about 100-fold variation in rate, amongst the contexts, particularly on substitutions of A and T. Rate heterogeneity of transitions differs from that of transversions, resulting in a more than 200-fold variation in the transitions:transversion bias. The data are consistent with a CpG effect, and it is shown that both the A+T content and the arrangement of purines/pyrimidines along the same DNA strand are correlated with rate variation. Expected equilibrium A+T content ranges from 36.4% to 82.8% across contexts, while G-C skew ranges from -77.4 to 72.2 and A-T skew from -63.9 to 68.2. The predicted equilibria are associated with specific features of the content of the hexanucleotide context, and also show close agreement with the observed context-dependent compositions. Finally, by controlling for the content of nucleotides closer to the substitution site it is shown that both the third and fourth nucleotide removed on each side of the substitution directly influence substitution dynamics at that site. Overall, the results demonstrate that noncoding sites in different contexts are evolving along very different evolutionary trajectories and that substitution dynamics are far more complex than typically assumed. This has important implications for a number of types of sequence analysis, particularly analyses of natural selection, and the context-dependent substitution matrices developed here can be applied in future analyses.</p>
Data in support of "Self-adaptive multi-objective climate policies align mitigation and adaptation strategies"
<p>The simulation model, the characterization of uncertainties, the calibration of the surrogate econometric damages model, and the simulation version of the FAIR climate model are available together with the optimization outputs and the scripts for replicating the figures of the paper.</p>
Artificial signal data for signal alignment testing.
<p>This is a set of signals-pairs, univariate and multivariate, that can be used to test alignment algorithms.</p>
Benchmark Datasets for Inductive Entity Alignment
<p>This upload contains datasets for benchmarking inductive entity alignment approaches.</p>
Highly significant improvement of protein sequence alignments with AlphaFold2
<p>Data, figures and tables from the manuscript "Highly significant improvement of protein sequence alignments with AlphaFold2" (https://doi.org/10.1093/bioinformatics/btac625).</p> <p>The repository containing all the steps to replicate the analysis is available at GitHub (https://github.com/cbcrg/msa-af2-nf).</p> <p>*The authors Athanasios Baltzis and Leila Mansouri contributed equally.</p>
Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone
<p>Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to <em>Haliotis virginea</em> Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: 1) the Three Kings Islands; 2) the Auckland, Chatham and Antipodes Islands; and 3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our non-reliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.</p>
ProgressiveMauve alignment of Xanthomonas oryzae pv. oryzae PXO35 assembly variants
<p>Archive containing the alignment of eight assembly variants using different assembly programs and sequencing technologies. This alignment has been produced by the progressiveMauve algorithm (<a href="https://doi.org/10.1371/journal.pone.0011147">https://doi.org/10.1371/journal.pone.0011147</a>). The main alignment file is "PXO35_assembly_comparison", which can be opened and viewed interactively using the mauve program (<a href="https://darlinglab.org/mauve/download.html">https://darlinglab.org/mauve/download.html</a>).</p>
Aligned and curated mtDNA sequences from: Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period
<p><strong><span>Aim: </span></strong><span>Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter-gatherers as the main cause. In contrast, the impact of humans on rodent populations </span><span>is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. </span><span>This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene.</span></p> <p><span><strong>Location:</strong> </span><span>Europe</span></p> <p><strong><span>Taxon: </span></strong><span>Common vole (<em>Microtus arvalis</em>)</span></p> <p><strong><span>Methods: </span></strong><span>We generated a dataset comprised of a 4.2-kb-long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated.</span></p> <p><span><strong>Results:</strong> </span><span>We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than previous estimates. </span><span>We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition.</span><span> </span><span>In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM), even at high latitudes.</span></p> <p><strong><span>Main conclusions: </span></strong><span>The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas </span><span>climate </span><span>deterioration </span><span>during</span><span> the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas.</span></p>
Alignement de Fillod, Port-aux-Français
Les Fillod, bâtiments préfabriqués en métal, ont été inventés par Ferdinand Fillod à partir des années 1920 à Florange. La modularité, le moindre coût et les facilités de transport et de montage de ces architectures les ont rendues particulièrement adaptées aux besoins des missions australes. Ces Fillod ont équipé les bases australes et antarctiques dès leur création. Les Fillod de cet alignement, devenues insalubres, ont été démantelées. Elles ont préalablement été analysées et numérisées par une mission patrimoine qui a permis leur conservation par l'étude. * Mission patrimoine 2017 : Virginie Motte (SRA, DAC Réunion) * Photogrammétrie : Abel Vaccaro (Nawar) * Topographie : Pierre Brial (OMT) Source: Objaverse 1.0 / Sketchfab
Supplementary material 2 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Set of 13 Euler/X toolkit output Maximally Informative Relations: Explanation note: Set of 13 Euler/X toolkit output Maximally Informative Relations (MIR) and alignment visualizations for the input data files provided in Suppl. material 1. Each output file is saved in. csv (MIR) and. pdf (alingments) format, respectively. Dryad. doi: 10.5061/dryad.53mv1
Supplementary material 1 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Set of 13 Euler/X toolkit input data files: Explanation note: Set of 13 Euler/X toolkit input data files for all alignments produced for Minyomerus [JF2015] use case (Figs 3, 4). Each file is saved in txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the corresponding figures. Dryad. doi: 10.5061/dryad.53mv1
Diatoms rbcL alignment and phylogeny
<p>The dataset contains:</p> <ul> <li>Reference rbcL alignment (604 sequences)</li> <li>Reference phylogeny reconstructed with RAxML (604 species)</li> </ul> <p> </p>
Reproduction package for the publication "Tidal disruption event AT2020ocn: early-time X-ray flares caused by a possible disc alignment process"
<p>This package contains the data analysed in the paper "Tidal disruption event AT2020ocn: early–time X–ray flares caused by a possible disc alignment process". The software XSPEC (Arnaud 1996) is needed to perform the spectral analysis and reproduce the results shown in the paper.</p> <p>The structure is as follows:</p> <p>./reproduction_ocn/nicer: contains all processed NICER data used in the paper, grouped by their epochs. "speclist-early.dat" lists all the early-time epochs before MJD 59130. "en_range.dat" lists the selected energy range at each epoch during the early-time period for X-ray spectral analysis. Within each epoch-specific folder, "src.fits" and "bkg.fits" are the source+background and background spectra re-binned using the FTOOL "ftgrouppha"; "*.arf" and "*.rmf" are ancillary file and response file for spectral analysis; rest files are direct products of the NICER data reduction process. See the paper for details.</p> <p>./reproduction_ocn/swift: contains all Swift/UVOT data used in the paper, grouped by their observation IDs. "m2.fits", "w1.fits", and "w2.fits" contain the UV lightcurves from three UV filters, produced by Swift task "uvotproduct". "swfxraypclc.dat" is the Swift/XRT lightcurve, produced by the online Swift pipeline: https://www.swift.ac.uk/user_objects/ (Evans et al. 2009). "./reproduction_ocn/MOSFiT-products/" includes MCMC products from the MOSFiT package (Mockler et al. 2019).</p> <p>./reproduction_ocn/xmm: contains the reduced XMM-Newton/EPIC-pn spectra of three epochs used in the paper. "1and2-slim.xcm" is fitting the XMM#1 and XMM#2 spectra using the slim disc model. "3-phenmnlgcl.xcm" and "3-relxillCp.xcm", are fitting the XMM#3 spectrum with, a powerlaw+zbbody model and a slim disc+relxillCp model, respectively.</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.