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1,199 results for “Alignement”
Sergestidae shrimp family single- and multi-gene alignments and tree files
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Multiple sequence alignments and phylogenetic trees from: Co-option of the limb patterning program in cephalopod eye development
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Prosopis laevigata microsatellite and sequence alignment data
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Combined alignment fasta file used for the phylogenetic analysis of Micropsalliota
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Stereodynamical control of the H+HD→H2+D reaction through HD reagent alignment
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Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.
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Virus alignments found in human cancer - Online Table
<p>The file contains three worksheets. The first one (OT1.1-Raw virus alignments) contains a complete list of all viral sequences detected in the study. The second (OT1.2-Filtering rules) describes rules for how raw alignments were filtered. The third (OT1.3-Viruses in cancer table) displays a table of viruses detected across cancers split by library type.</p> <p> </p> <p>OT1.1-Raw virus alignments</p> <p>"reason" (column AF): the value "a10m5" is a specific filter criterion we employed. If the number of alignments (column J) is fewer than 10 or if the MAPQ score (column K) is less than 5, the "keep" column is set to "no" and the "reason" is indicated as "a10m5". </p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "Description and phylogenetic relationships of a new trans-Andean species of Elachistocleis Parker 1927 (Amphibia, Anura, Microhylidae)"
<p>Aligned DNA sequence matrix for phylogenetic analyses in the article "Description and phylogenetic relationships of a new trans-Andean species of <em>Elachistocleis</em> Parker 1927 (Amphibia, Anura, Microhylidae)"</p> <p>Gene partitions are arranged as follows (tRNAs are included as part of larger adjacent genes):</p> <p>16S = 1-1165;<br> BDNFcodonPos1 = 1166 - 1874\3;<br> BDNFcodonPos2 = 1167 - 1875\3;<br> BDNFcodonPos3 = 1168 - 1876\3;<br> cmyccodonPos1 = 1878 - 2319\3;<br> cmyccodonPos2 = 1879 - 2320\3;<br> cmyccodonPos3 = 1877 - 2318\3;<br> CO1codonPos1 = 2321 - 2981\3;<br> CO1codonPos2 = 2322 - 2979\3;<br> CO1codonPos3 = 2323 - 2980\3;<br> histcodonPos1 = 2983 - 3307\3;<br> histcodonPos2 = 2984 - 3308\3;<br> histcodonPos3 = 2982 - 3309\3;<br> siacodonPos1 = 3311 - 3704\3;<br> siacodonPos2 = 3312 - 3705\3;<br> siacodonPos3 = 3310 - 3706\3;<br> tyrcodonPos1 = 3708 - 4263\3;<br> tyrcodonPos2 = 3709 - 4264\3;<br> tyrcodonPos3 = 3707 - 4262\3;<br> 28S = 4265-5084;<br> 12S = 5085-6171;</p> <p> </p>
Instructional Video: Metashape - Upload and Align Images
<p>https://www.youtube.com/watch?v=oY-7NuAaD1M&t=98s</p>
Supplementary data for the manuscript "Flow and Entrainment Mechanisms around a Freshwater Mussel Aligned with the Incoming Flow"
<p>This repository is associated with the manuscript for Water Resource Research (WRR): Flow and Entrainment Mechanisms around a Freshwater Mussel Aligned with the Incoming Flow. The repository contains the data files for the manuscript.</p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "Three new species of frogs of the genus Pristimantis (Anura: Strabomantidae) with a redefinition of the P. lacrimosus species group"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Three new species of frogs of the genus Pristimantis (Anura: Strabomantidae) with a redefinition of the P. lacrimosus species group". The matrix is in NEXUS format.</p> <p>Gene partitions are arranged as follows (tRNAs are included as part of larger adjacent genes):</p> <p>RAG1 codon position 1 = 1-625\3;<br> RAG1 codon position 2 = 2-626\3;<br> RAG1 codon position 3 = 3-627\3;<br> 12S rRNA = 628-1440;<br> 16S rRNA = 1441-3071;<br> ND1 codon position 1 = 3072-3972\3;<br> ND1 codon position 2 = 3073-3973\3;<br> ND1 codon position 3 = 3074-3974\3;</p>
Simulated pairs of nucleotide sequences for testing (alignment-free) genome distance estimate methods
<p>This repository contains 24,000 pairs of nucleotide sequences (and associated parameters) that have been simulated for testing alignment-free genome distance estimates. Given an evolutionary distance <em>d</em> varying from 0.05 to 1.00 nucleotide substitutions per character (step = 0.05), the program <a href="http://abacus.gene.ucl.ac.uk/software/indelible/"><em>INDELible</em></a> was used to simulate the evolution of 200 nucleotide sequence pairs with <em>d</em> substitution events per character under the models GTR and GTR+Γ. Each model was adjusted with three different equilibrium frequencies:</p> <ul> <li><em>f</em><sub>1</sub>: equal frequencies, i.e. freq(A) = freq(C) = freq(G) = freq(T) = 0.25,</li> <li><em>f</em><sub>2</sub>: GC-rich, i.e. freq(A) = 0.1, freq(C) = 0.3, freq(G) = 0.4, freq(T) = 0.2,</li> <li><em>f</em><sub>3</sub>: AT-rich, i.e. freq(A) = freq(T) = 0.4, freq(C) = freq(G) = 0.1.</li> </ul> <p>For each simulated sequence pair, model parameters (i.e. GTR: six relative rates of nucleotide substitution; GTR+Γ: six rates and one Γ shape parameter) were randomly drawn from 142 sets of parameters derived from real-case data (see file <a href="https://zenodo.org/record/4034261/files/GTR.params.trees.tsv?download=1">GTR.params.trees.tsv</a> at <a href="https://zenodo.org/record/4034261">https://zenodo.org/record/4034261</a>). Initial sequence length was 5 Mbs, and an indel rate of 0.01 was set with indel length drawn from [1, 50000] according to a Zipf distribution with parameter 1.5 (see <em>INDELible</em> <a href="http://abacus.gene.ucl.ac.uk/software/indelible/manual/model.shtml">manual</a>).</p> <p> </p> <p>For each of the 20 evolutionary distances <em>d</em> = 0.05, 0.10, ..., 1.00, six XZ-compressed files containing 200 simulation data are available:</p> <ul> <li><code>data-d-f1-nogam.tsv.xz</code> data simulated under the model GTR with equilibrium frequencies <em>f</em><sub>1</sub></li> <li><code>data-d-f1-gamma.tsv.xz</code> data simulated under the model GTR+Γ with equilibrium frequencies <em>f</em><sub>1</sub></li> <li><code>data-d-f2-nogam.tsv.xz</code> data simulated under the model GTR with equilibrium frequencies <em>f</em><sub>2</sub></li> <li><code>data-d-f2-gamma.tsv.xz</code> data simulated under the model GTR+Γ with equilibrium frequencies <em>f</em><sub>2</sub></li> <li><code>data-d-f3-nogam.tsv.xz</code> data simulated under the model GTR with equilibrium frequencies <em>f</em><sub>3</sub></li> <li><code>data-d-f3-gamma.tsv.xz</code> data simulated under the model GTR+Γ with equilibrium frequencies <em>f</em><sub>3</sub></li> </ul> <p> </p> <p>Each file is tab-delimited and contains the 18 following fields:</p> <ul> <li><code>[1] </code> integer <em>seed</em> value specified to <em>INDELible</em>,</li> <li><code>[2-5] </code> frequencies of T, C, A, G, respectively, specified to <em>INDELible</em>,</li> <li><code>[6-10] </code> C-T, A-T, G-T, A-C, C-G rate parameters, respectivly (normalized such that A-G rate = 1), specified to <em>INDELible</em>,</li> <li><code>[11] </code> Γ shape parameter <em>alpha</em> (= 0 in the <code>nogam</code> files, i.e. GTR substitution model without Γ) specified to <em>INDELible</em>,</li> <li><code>[12] </code> length <em>lgt1</em> of the first sequence <em>seq1</em> (i.e. no. A, C, G, T in <em>seq1</em>),</li> <li><code>[13] </code> length <em>lgt2</em> of the second sequence <em>seq2</em> (i.e. no. A, C, G, T in <em>seq2</em>),</li> <li><code>[14] </code> no. <em>sites</em> in aligned sequences <em>seq1</em> and <em>seq2</em> (i.e. no. A, C, G, T and gap character states in <em>seq1</em> or <em>seq2</em>),</li> <li><code>[15] </code> no. non-gapped sites (<em>core</em> sites) in aligned sequences <em>seq1</em> and <em>seq2</em>,</li> <li><code>[16] </code> observed <em>p-distance</em> between aligned sequences <em>seq1</em> and <em>seq2</em> (i.e. no. nucleotide mismatches divided by no. <em>core</em> sites),</li> <li><code>[17] </code> aligned <em>seq1</em> (containing indel gaps),</li> <li><code>[18] </code> aligned <em>seq2</em> (containing indel gaps).</li> </ul> <p>Of note, <em>seq1</em> and <em>seq2</em> (fields <code>[17-18]</code>) being aligned, these two entries are two strings with identical no. <em>sites</em> (field <code>[14]</code>). Gap character states (<code>-</code>) should be removed from <em>seq1</em> and <em>seq2</em> to obtain the unaligned sequences.</p> <p>_____</p> <p>Criscuolo A (2020) <em>On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference</em>. F1000Research, 9:1309. <a href="https://doi.org/10.12688/f1000research.26930.1">doi:10.12688/f1000research.26930.1</a></p>
Supplementary material 1 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S1 – Training, test, and validation data sets used in model training and analysis
Alignment used for the phylogenies of "The earliest diverging extant scleractinian corals recovered by mitochondrial genomes"
<p>Alignment of scleractinian corals based on mitochondrial genomes and including species of the family Micrabaciidae. This alignment was used for running Maximum Likelihood and Bayesian Inference phylogenies. "tree02_alignment.phy" refers to the actual alignment while "tree02_alignment.partitions.txt" indicates where each gene partition begins/ends.</p>
Figure 2 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 2 The current and required implementation readiness levels for DiSSCo to enter the construction phase of the DiSSCo RI. The grey arrows indicate the tasks for the DiSSCo Prepare project.
Figure 3 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 3 An example of a simple Digital Specimen (Hardisty 2020). Arrows point to identifiers of linked information that was derived from or is related to the physical specimen it represents. dissco.tech blog post.
Figure 4 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 4 The links and interactions between the EEA, ETCs (European Topic Centres), NFPs (National Focal Points), and NRCs (National Reference Centres) - image from EEA website*25.
Data from: Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment
Reduced-representation genome sequencing such as RADseq aids the analysis of genomes by reducing the quantity of data, thereby lowering both sequencing costs and computational burdens. RADseq was initially designed for studying genetic variation across genomes at the population level, but has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data. Alignment-free methods are both efficient and accurate for phylogenetic reconstructions with whole genomes and are especially practical for non-model organisms; nonetheless, alignment-free methods have not been applied with reduced genome sequencing data. Here, we test a full-genome assembly and alignment-free method, AAF, in application to RADseq data and propose two procedures for reads selection to remove reads from restriction sites that were not found in taxa being compared. We validate these methods using both simulations and real datasets. Reads selection improved the accuracy of phylogenetic construction in every simulated scenario and the two real datasets, making AAF as good or better than a comparable alignment-based method, even though AAF had much lower computational burdens. We also investigated the sources of missing data in RADseq and their effects on phylogeny reconstruction using AAF. The AAF pipeline modified for RADseq or other reduced-representation sequencing data, phyloRAD, is available on github (https://github.com/fanhuan/phyloRAD).
Data from: Assessing the alignment of sexual and natural selection using radio-mutagenized seed beetles
A major unsolved question in evolutionary biology concerns the relationship between natural and sexual selection. Sexual selection might augment natural selection, e.g. if mutations that harm female fecundity also reduce male mating success. Conversely, sexual selection might favor traits that impair naturally-selected fitness components. We induced detrimental mutations in Callosobruchus maculatus beetles using X-ray irradiation, and then experimentally measured the effect of pre-copulatory sexual selection on offspring number and survival rate. Sexual selection treatment had a negative effect on egg-to-adult survivorship, though the number of progeny reaching adulthood was unaffected, perhaps because eggs and juveniles that failed to develop lessened competition on the survivors. We hypothesize that the negative effect of sexual selection arose because sexually competitive males transmitted a smaller nuptial gift, or carried alleles that conferred reduced survival. Although we found no evidence that sexual selection on males can purge alleles that are detrimental to naturally-selected fitness components, such benefits might exist in other environmental or genetic contexts.
Data from: The core planar cell polarity gene, Vangl2, directs adult corneal epithelial cell alignment and migration
This study shows that the core planar cell polarity (PCP) genes direct the aligned cell migration in the adult corneal epithelium, a stratified squamous epithelium on the outer surface of the vertebrate eye. Expression of multiple core PCP genes was demonstrated in the adult corneal epithelium. PCP components were manipulated genetically and pharmacologically in human and mouse corneal epithelial cells in vivo and in vitro. Knockdown of VANGL2 reduced the directional component of migration of human corneal epithelial (HCE) cells without affecting speed. It was shown that signalling through PCP mediators, dishevelled, dishevelled-associated activator of morphogenesis and Rho-associated protein kinase directs the alignment of HCE cells by affecting cytoskeletal reorganization. Cells in which VANGL2 was disrupted tended to misalign on grooved surfaces and migrate across, rather than parallel to the grooves. Adult corneal epithelial cells in which Vangl2 had been conditionally deleted showed a reduced rate of wound-healing migration. Conditional deletion of Vangl2 in the mouse corneal epithelium ablated the normal highly stereotyped patterns of centripetal cell migration in vivo from the periphery (limbus) to the centre of the cornea. Corneal opacity owing to chronic wounding is a major cause of degenerative blindness across the world, and this study shows that Vangl2 activity is required for directional corneal epithelial migration.
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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.