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1,199 results for “Alignement”
Machine learning for predicting the average length of vertically aligned TiO2 nanotubes. Dataset Description
<p>Machine learning for predicting the average length of vertically aligned TiO2 nanotubes. Dataset Description. Dataset is found in two versions: MATLAB mat file and CSV format. Rows contains samples and Columns Features. Last Column represents the Response variable.</p>
A Soft Alignment Model for Bug Deduplication
<p>This repository contains data used in the paper: <strong>A Soft Alignment Model for Bug Deduplication</strong> <em>by Irving Muller Rodrigues, Daniel Aloise, Eraldo Rezende Fernandes, and Michel Dagenais.</em></p>
Interaction between nighttime MSTID and mid-latitude field-aligned plasma depletion over the transition region of geomagnetic low-mid latitude: First results from Hanle, India
<p>630.0 nm airglow emission data from Hanle all-sky imager</p> <p>Hnale GPS TEC</p> <p>New Delhi Ionograms</p> <p>GIRI Radar Data</p>
Reference transcriptome and Alignments of candidate gene
<p>Recently diverged taxa with contrasting phenotypes offer opportunities for unravelling the genetic basis of phenotypic variation in nature. Horseshoe bats are a speciose group that exhibit a derived form of high duty cycle echolocation in which the inner ear is finely tuned to echoes of the narrowband call frequency. Here, by focusing on three recently diverged subspecies of the intermediate horseshoe bat (<i>Rhinolophus affinis</i>) that display divergent echolocation call frequencies, we aim to identify candidate loci putatively involved in hearing frequency variation. We used <i>de novo</i> transcriptome sequencing of two mainland taxa (<i>himalayanus</i> and <i>macrurus</i>)<i> </i>and one island taxon (<i>hainanus</i>) to compare expression profiles of thousands of genes. By comparing taxa with divergent call frequencies (around 15 kHz difference), we identified 252 differentially expressed genes (DEGs), of which six have been shown to be involved in hearing or deafness in human/mouse. To obtain further validation of these results, we applied quantitative reverse transcription-PCR to the candidate gene <i>FBXL15</i> and found a broad association between the level of expression and call frequency across taxa. The genes identified here represent strong candidate loci associated with hearing frequency variation in bats.</p>
Blastocystis SSU rRNA alignment
<p><i>Blastocystis</i> is a cosmopolitan protist inhabiting the human intestine; which prevalence varies between non-industrial and industrialized countries. Its role in the human gut ecosystem remains unclear due to persisting gaps in knowledge of epidemiology and factors affecting gut colonization. The aim of this study was therefore to expand the knowledge of the epidemiology of <i>Blastocystis</i> in the gut-healthy humans in one of the industrialized European countries, including the distribution of its subtypes, the correlation between its occurrence and several factors such as lifestyle, contact with animals, age and sex. A total of 288 stool samples were obtained from non-symptomatic individuals over the entire age-range and 136 samples from animals with which the volunteers were in frequent contact. All samples were examined in parallel by PCR and xenic culture. <i>Blastocystis</i> was detected in samples from both human and non-human hosts. In humans, the overall prevalence was 24% and eight subtypes were found, whereas in animals the prevalence was 10% and only five subtypes were detected. For factors, there was a higher incidence of <i>Blastocystis</i> in individuals traveling outside Europe who were in frequent contact with livestock and over 50 years of age. We found no effect on gender.</p>
Simulated nucleotide sequences for testing alignment-free genome distance estimates
<p>This repository contains (12×500=)6,000 pairs of nucleotide sequences that have been simulated for testing alignment-free genome distance estimates, as described in <a href="https://riojournal.com/article/36178/">Criscuolo (2019)</a>. Given an evolutionary distance <em>d</em> varying from 0.05 to 0.60 (step = 0.05), the program <a href="http://tree.bio.ed.ac.uk/software/seqgen/">SeqGen</a> was used to simulate the evolution of 500 nucleotide sequence pairs with <em>d</em> substitution events per character (GTR+Γ evolutionary model).</p> <p>For each of the 12 evolutionary distances <em>d</em> = 0.05, 0.10, ..., 0.60, an XZ-compressed file containing 500 lines is available. Each line contains 18 fields separated by blank spaces:<br> [1] seed value used during simulation,<br> [2] true evolutionary distance <em>d</em> between the two simulated sequences,<br> [3] total number of simulated characters,<br> [4] number of non-indel characters with nucleotide mismatch,<br> [5] number of non-indel characters,<br> [6-9] A, C, G, T frequencies used during simulation,<br> [10-15] GTR parameters used during simulation,<br> [16] Γ distribution parameter used during simulation,<br> [17-18] two simulated sequences with indel events as gaps.</p> <p>Of note, each pair of aligned sequences without gaps can be regenerated using <a href="http://tree.bio.ed.ac.uk/software/seqgen/">SeqGen</a> v1.3.4 with parameters from fields [1,3,6-16] and the following two-leaf model tree:</p> <pre>(t1:d,t2:0.000);</pre> <p>where <em>d</em> is given in field [2].</p> <p>___</p> <p>Criscuolo A (2019) <em>A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies</em>. Research Ideas and Outcomes, 5:e36178. doi:<a href="https://doi.org/10.3897/rio.5.e36178">10.3897/rio.5.e36178</a></p>
Figure 1 from: Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller EK, Schulman L, Tilley L, Robertson T (2020) White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). Research Ideas and Outcomes 6: e62361. https://doi.org/10.3897/rio.6.e62361
Figure 1 The DiSSCo programme with all strategically aligned projects.
Tree and amino acid alignments of thioredoxin, glucose-6-phosphate dehydrogenase, and malate dehydrogenase
<p>Redox regulation in phytoplankton is critical to monitor and stabilize metabolic pathways under changing environmental conditions. In plastids, the thioredoxin (TRX) system is linked to photosynthetic electron transport and fine tuning the metabolism to fluctuating light levels. Expansion of the number of redox signal transmitters and their protein targets, as seen in plants, is believed to increase cell robustness. In this study, we searched for genes related to redox regulation in the genome of the photosynthetic amoeba <i>Paulinella micropora </i>KR01 (hereafter, KR01). The genus <i>Paulinella </i>includes testate filose amoebae, in which a single clade acquired a photosynthetic organelle, the chromatophore, from an alpha cyanobacterial donor<i>. </i>This independent primary endosymbiosis occurred relatively recently (~ 124 Ma), when compared to Archaeplastida (> 1 Ga), making photosynthetic <i>Paulinella </i>a valuable model for studying the earlier stages of primary endosymbiosis.<i> </i>Our comparative analysis demonstrates that this lineage has<i> </i>evolved a thioredoxin system similar to that from other algae, relying however on genes with diverse phylogenetic origins (i.e., the endosymbiont, host, bacteria, red algae). One TRX of eukaryotic provenance is targeted to the chromatophore, implicating host-endosymbiont coordination of redox regulation. A chromatophore targeted glucose-6-phosphate dehydrogenase of red algal origin suggests that <i>Paulinella </i>exploited the existing redox regulation system in Archaeplastida to foster integration. Our study elucidates the independent evolution of the thioredoxin system in photosynthetic <i>Paulinella</i>, whose parts derive from the existing genetic toolkit in diverse organisms.</p>
Concurrent observations of plasma bubbles and field-aligned irregularities in low-latitudes of China
<p>These figures show the raw and processed data of the 630 nm all-sky airglow imager from Fuke Observatory in Hainan Province, China at 16:54-19:23 UT on September 23, 2014 and 15:00-16:33 UT on April 13, 2015, respectively, with a temporal resolution of 3 min.</p>
Archaea and Frankia gene family alignments and associated scripts
<p>Biological datasets (gene family alignments from Archaea and Frankia) associated with the manuscript titled "A systematic assessment of phylogenomic approaches for microbial species tree reconstruction" by S. Weiner, Y. Feng, J. P. Gogarten, and M. S. Bansal. A preprint of the manuscript is available from: <span>https://doi.org/10.1101/2024.11.20.624597</span></p>
RNA Seq STAR Aligner
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Sequence alignments for ITS, rpl16, and trnL-trnF
<p>The two data files consist of sequence alignments in FASTA format. The file 'Distichium_alignment_ITS.txt' is the alignment used for the analysis resulting in the network in Fig. 1A in the paper and the file 'Distichium_alignment_3 markers.txt' is the alignment used for the analysis resulting in the network in Fig. 1B. The GenBank numbers corresponding with the sequence numbers can be found in Appendix 1 in the paper.</p>
Multiple Sequence Alignments of primate proteomes
<p>This image dataset contains Multiple Sequence Alignments of protein sequences extracted from the Uniprot reference proteomes and RefSeq databases. </p>
more data for "High-Latitude Electrodynamics Specified in SAMI3 Using AMPERE Field-Aligned Currents"
<p>Potential maps derived from AMPERE field-aligned current data and SAMI3 conductances</p>
Data from: Influence of alignment on the mtDNA phylogeny of Cetacea: questionable support for a Mysticeti/Physeteroidea clade
[No abstract entered]
Alignment of GeCo2O4 sample 2017/09/07
<p>Alignment of GeCo2O4 sample</p>
Murine Cortex M6A Epitranscriptomic Values for Aligned MM39, Mitochondrial, and Calibration Reads
Open the record for dataset details and reuse information.
Aligned Long-Read Murine Samples: Part 29
<p>Accession numbers can be queried via the European Nucleotide Archive for metadata information: https://www.ebi.ac.uk/ena </p> <p>Samples analyzed via the original version of L-RAPiT: </p> <p>Nelson, T.M.; Ghosh, S.; Postler, T.S. L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data. <em>Int. J. Mol. Sci.</em> <strong>2022</strong>, <em>23</em>, 15851. https://doi.org/10.3390/ijms232415851</p>
Aligned Long-Read Murine Samples: Part 28
<p>Accession numbers can be queried via the European Nucleotide Archive for metadata information: https://www.ebi.ac.uk/ena </p> <p>Samples analyzed via the original version of L-RAPiT: </p> <p>Nelson, T.M.; Ghosh, S.; Postler, T.S. L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data. <em>Int. J. Mol. Sci.</em> <strong>2022</strong>, <em>23</em>, 15851. https://doi.org/10.3390/ijms232415851</p>
Aligned Long-Read Murine Samples: Part 26
<p>Accession numbers can be queried via the European Nucleotide Archive for metadata information: https://www.ebi.ac.uk/ena </p> <p>Samples analyzed via the original version of L-RAPiT: </p> <p>Nelson, T.M.; Ghosh, S.; Postler, T.S. L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data. <em>Int. J. Mol. Sci.</em> <strong>2022</strong>, <em>23</em>, 15851. https://doi.org/10.3390/ijms232415851</p>
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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.