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1,199 results for “Alignement”
Aligned Long-Read Murine Samples: Part 3
<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 1
<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 7
<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 6
<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 2
<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 5
<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>
Validation data for tttsa, automated tilt-series alignment in PyTorch
<p>This dataset contains a tilt-series ordered by tilt angle saved in mrc format (.st), and the corresponding tilt angles for the collection (.rawtlt). The approximate tilt-axis angle was -88.7 in the serial-em mdoc file.</p> <p>The dataset also contains a bash script to run AreTomo (v1.3.4) for the same tilt-series and an output alignment from AreTomo (.aln).</p>
Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation
<p>Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic datasets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated haploid and polyploid short-read sequences with various levels of missing data. Mash-based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyze publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems or those with only poor quality sequence data available.</p>
group-1-EF alignment and SNPs
<p>Alignment of reads for the BSA bulk 'early flowering' (EF) against the <em>B. oleracea</em> reference genome (as BAM file), and subsequent SNP calling results (as compressed VCF file).</p>
Tree and sequence alignment used for diet reconstruction of Laurasiatheria
<p><b>Background:</b> Laurasiatheria contains taxa with diverse diets, while the molecular basis and evolutionary history underlying their dietary diversification are less clear.</p> <p><b>Results:</b> In this study, we used the recently developed molecular phyloecological approach to examine the adaptive evolution of digestive system-related genes across both carnivorous and herbivorous mammals within Laurasiatheria. Our results show an intensified selection of fat and/or protein utilization across all examined carnivorous lineages, which is consistent with their high-protein and high-fat diets. Intriguingly, for herbivorous lineages (ungulates), which have a high-carbohydrate diet, they show a similar selection pattern as that of carnivorous lineages. Our results suggest that for the ungulates, which have a specialized digestive system, the selection intensity of their digestive system-related genes does not necessarily reflect loads of the nutrient components in their diets but appears to be positively related to the loads of the nutrient components that are capable of being directly utilized by the herbivores themselves. Based on these findings, we reconstructed the dietary evolution within Laurasiatheria, and our results reveal the dominant carnivory during the early diversification of Laurasiatheria. In particular, our results suggest that the ancestral bats and the common ancestor of ruminants and cetaceans may be carnivorous as well. We also found evidence of the convergent evolution of one fat utilization-related gene, <i>APOB</i>, across carnivorous taxa.</p> <p><b>Conclusions: </b>Our molecular phyloecological results suggest that digestive system-related genes can be used to determine the molecular basis of diet differentiations and to reconstruct ancestral diets. </p>
Figure 9 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
Figure 9 - Habitus of Minyomerus laticeps [JF2015], female A lateral view B dorsal view.
Figure 47 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
Figure 47 - Habitus of Minyomerus rutellirostris [JF2015], male A lateral view B dorsal view.
Figure 5 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
Figure 5 - Habitus of Minyomerus imberbus [JF2015], female A dorsal view B lateral view.
Figure 41 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
Figure 41 - Habitus of Minyomerus gravivultus [JF2015], female A lateral view B dorsal view.
Figure 38 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
Figure 38 - Habitus of Minyomerus politus [JF2015], female A lateral view B dorsal view.
Figure 44 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
Figure 44 - Habitus of Minyomerus griseus [JF2015], male A dorsal view B lateral view.
Figure 39 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
Figure 39 - Habitus of Minyomerus politus [JF2015], male A lateral view B dorsal view.
Figure 36 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
Figure 36 - Habitus of Minyomerus bulbifrons [JF2015], female A lateral view B dorsal view.
Figure 34 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
Figure 34 - Habitus of Minyomerus puticulatus [JF2015], male A lateral view B dorsal view.
Figure 46 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
Figure 46 - Habitus of Minyomerus rutellirostris [JF2015], female A lateral view B dorsal view.
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.