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175 results for “sequence alignments”
AliSim: Ultrafast and Realistic Sequence Alignment Simulator for Phylogenetics - Supplementary Data
<p>This supplementary data contains testing scripts, input/output data for validating and benchmarking AliSim.</p>
Cephalopod retinal development shows vertebrate-like mechanisms of neurogenesis: Multiple sequence alignments and phylogenetic trees
<p>Coleoid cephalopods, including squid, cuttlefish and octopus, have large and complex nervous systems and camera-type eyes that are comparable only to features that have independently evolved in the vertebrate lineage. The changes in development that result in the evolution of nervous system size and diversity of neural cell-types are not well understood. Here, we have pioneered live-imaging techniques and performed functional interrogation to show the squid, <em>Doryteuthis</em> <em>pealeii</em>, utilizes mechanisms during retinal neurogenesis that are hallmarks of vertebrate processes. Given the convergent evolution of elaborate visual systems in cephalopods and vertebrates, these results reveal common mechanisms that underlie the growth of highly proliferative neurogenic primordia that may alter ontogenetic allometry and contribute to the evolution of complex nervous systems.</p>
Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals
<p><span>Narrow-headed vole, together with collared lemming and common vole, was the most abundant small mammal species across Eurasian Late Pleistocene steppe-tundra environments. Previous ancient DNA studies of </span><span>the latter</span><span> </span><span>two</span><span> revealed dynamic past population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary </span><span>histories,</span><span> we generated a dataset comprising mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from multiple sites across Europe and north-</span><span>western</span><span> Asia and covering the last ca. 100 thousand years (ka). We inferred Bayesian time-aware phylogenies using 11 </span><span>radiocarbon-dated</span><span> samples for calibration of the molecular clock. We found that across the three </span><span>species,</span><span> divergence of the main mtDNA lineages occurred during Marine Isotope Stages (MIS) 7 and MIS 5, suggesting a common response </span><span>of species adapted to open habitat to the interglacial environments. </span><span>In European narrow-headed voles, we identified multiple </span><span>time-structured</span><span> mtDNA lineages, implying lineage turnovers. Timing of some of these turnovers was synchronous across all three </span><span>species,</span><span> allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.</span></p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "A new species of spiny-backed tree frog, genus Osteocephalus (Anura: Hylidae), from the Yanachaga Chemillén National Park in central Peru"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"</p> <p>The matrix is in NEXUS format and has 14791 bp and 38 terminals.</p> <p>Partitions are as follows:</p> <p>charset 12S_16S = 1-2442;<br> charset mtGenome_other_genes = 2443-9180; charset nonCoding = 3132- 3138 4776- 4857 5203- 5214;<br> charset codonPos1 = 2443-3130\3 3139-4774\3 4858-5200\3 5215-9178\3;<br> charset codonPos2 = 2444-3131\3 3140-4775\3 4859-5201\3 5216-9179\3;<br> charset codonPos3 = 2445-3129\3 3141-4773\3 4860-5202\3 5217-9180\3;<br> charset 16S_ND1nonCoding = 9181- 9428 10390- 10506 ;<br> charset 16S_ND1codonPos1 = 9429-10389\3;<br> charset 16S_ND1codonPos2 = 9430-10387\3;<br> charset 16S_ND1codonPos3 = 9431-10388\3;<br> charset POMCcodonPos1 = 10507-11068\3;<br> charset POMCcodonPos2 = 10508-11066\3;<br> charset POMCcodonPos3 = 10509-11067\3;<br> charset CO1codonPos1 = 11069-12608\3;<br> charset CO1codonPos2 = 11070-12609\3;<br> charset CO1codonPos3 = 11071-12610\3;<br> charset CytbcodonPos1 = 12611-13757\3;<br> charset CytbcodonPos2 = 12612-13758\3;<br> charset CytbcodonPos3 = 12613-13759\3;<br> charset ND2codonPos1 = 13760-14789\3;<br> charset ND2codonPos2 = 13761-14790\3;<br> charset ND2codonPos3 = 13762-14791\3;</p>
Multiple sequence alignments of newly reconstructed and published cervid and human mtDNA
<p><span>Assigning prehistoric objects to specific individuals is usually impossible outside of burial contexts. Here we present a non-destructive method for gradually releasing DNA from ancient bone and tooth artifacts. Application of the method to an Upper Paleolithic deer tooth pendant from Denisova Cave (Russia) resulted in the recovery of DNA from both the deer and a female human individual. Genetic dates obtained from the deer and human mitochondrial genomes estimate the age of the pendant at approximately 20,000 to 24,000 years. Nuclear DNA from its presumed maker or wearer shows strong affinities to contemporaneous Ancient North Eurasian individuals previously found further east in Siberia. Our work opens up new possibilities for linking cultural and genetic records in prehistoric archaeology.</span></p>
extHomFam v37.0: structural benchmark for protein multiple sequence alignments
<p>extHomFam v37.0 was constructed by combining Homstrad reference alignments (2 December 2023 release) with Pfam 37.0 (UniProt release) families containing at least 200 sequences. Homstrad entries with less than 3 reference sequences and those pointing to dead Pfam families were discarded.</p> <p> </p>
Multiple sequence alignment for the native Norwegian vascular plant phylogeny
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Multiple sequence alignments of newly reconstructed and published cervid and human mtDNA
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DNA sequences of transgenes detected via environmental DNA (raw ABI files, processed FASTA files, and reference alignments)
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.bam alignment files of Illumina and ONT sequencing of pREF plasmid
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Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals
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Alignments of ITS1 gene sequences from Harpacticella inopinata
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Cephalopod retinal development shows vertebrate-like mechanisms of neurogenesis: Multiple sequence alignments and phylogenetic trees
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Alignment of mitogenome sequences (FASTA file) for a paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies
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List of known SNP positions (based on SNP chip data) for base quality score recalibration of alignments for whole-genome resequencing and whole-genome bisulfite sequencing data from great tits (Parus major)
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Alignments of reindeer/caribou mitogenome sequences
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Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments
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Aligned DNA sequence matrix for phylogenetic analyses in the article "Fifty years after: a taxonomic revision of the amphibian species from the Ecuadorian biodiversity hotspot Abra de Zamora, with description of two new Pristimantis species"
<p>The aligned matrices are in fasta format. Genes are arranged as follows:</p> <p>Subgenus Huicundomantis (Huicundomantis.fas):</p> <p>12S = 1–905</p> <p>16S = 906–1820</p> <p>RAG-1 = 1821–2463</p> <p> </p> <p>Genus Lynchius (Lynchius.fas):</p> <p>12S = 1–1028</p> <p>16S = 1029–2313</p> <p>RAG-1 = 2314–2925</p> <p> </p> <p>Pristimantis orestes group (Pristimantis_orestes.fas):</p> <p>12S = 1–964</p> <p>16S = 965–2041</p> <p>RAG-1 = 2042–2683</p>
Multiple alignment of DNA-B sequences from EACMV, EACMKV, EACMMV, EACMZV, SACMV (5 "species")
<p>All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl (A. Rambaut) and AliView (A. Larsson).</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Multiple alignment of ICMV and SLCMV DNA-B sequences
<p>All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl and AliView.</p> <p>Note added 2020-09-07: AJ575821 is listed in the file as ICMV based on its assignment in the NCBI Taxonomy database (taxa 341701 and 31600) but it is better classified as SLCMV.</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</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.