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1,199 results for “Alignement”
CATH-KinFams: CATH Protein Kinase classification alignments and Hidden Markov Models
<p>CATH KinFams are protein kinase domain families classified according to functional similarity based on SDP. In this deposition we make available 2,210 KinFams sequence alignments alongside Hidden Markov Models built from them to be used with HMMER3.</p> <p>A concatenated library 'kinases_4.3-FF-seed.hmm' is also available to scan against the whole KinFams dataset.</p> <p>The Zenodo deposition contains:</p> <p>kinfams-cath-4.3-seed-alignments.tar.gz - KinFams FASTA file alignments with headers 'UniProt_ID/start-stop' i.e. A8XMX4/281-587</p> <p>kinfams-cath-4.3-seed-hmms.tar.gz - HMMs for each individual KinFam and concatenated in a HMM library.</p> <p>kinfams-cath-4.3-seed-mda-strings - Multi-Domain-Architecture string assignment for each sequence in the KinFams dataset.</p> <p>human_kinfams_af2_models_cif.tar.gz - Chopped mmCIF files containing Human Kinases AlphaFold2 Models.</p>
Dataset of NaOsO3 nanopillar alignment from PX I (Swiss Light Source)
<p>Dataset of NaOsO3 nanopillar alignment from PX I (Swiss Light Source)</p>
Alignment: A new, putatively semisubterranean, Rhithrodytes diving beetle from Southwestern Sardinia (Coleoptera: Dytiscidae: Hydroporini)
<p>Alignment for the molecular analyses made in the publication A new, putatively semisubterranean, <em>Rhithrodytes </em>diving beetle from Southwestern Sardinia (Coleoptera: Dytiscidae: Hydroporini).</p>
genome alignment of 88 speceis
<p>genome alignment of 88 speceis</p>
VCF of structural variant calls of Nanopore data aligned to dm6 reference genome
<p>Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the <em>dl</em>-<em>49</em> <em>chrX</em> inversion in <em>D</em>. <em>melanogaster</em>. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs are completely suppressed within 500 kb of inversion breakpoints, are severely reduced within 2 Mb of an inversion breakpoint, and increase above wildtype levels 2–4 Mb from the breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, occur at wild-type levels near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break location or frequency. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.</p>
Alignments of PSGs along with the crucial primate nodes
<p><span>Comparative analysis of primate genomes within a phylogenetic context is crucial for understanding the evolution of human genetic architecture and the diversity of primates. Here, we present a phylogenomic study of </span><span>50</span><span> primate species spanning </span><span>38</span><span> genera and </span><span>14</span><span> families, including 27 new genomes first reported in this </span><span>study</span><span> with many from previously less represented groups, the New World monkeys and </span><span>Strepsirrhini</span><span>. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes were under positive selection in different lineages that have roles in the nervous, skeletal and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals many key genomic innovations occurred in the </span><span>Simiiformes</span><span> ancestral node that may have profound impacts on the radiation of Simiiformes and human evolution.</span></p>
Madrepora_UCE_alignment
<p>UCEs alignment for Madrepora</p>
Aligned Diffusion Schroedinger Bridges
<p>We add the processed and prepared raw datasets for the D3PM dataset.</p> <p><br> <strong>Paper Abstract</strong><br> Diffusion Schrödinger bridges (DSB) have recently emerged as a powerful framework for recovering stochastic dynamics via their marginal observations at different time points. Despite numerous successful applications, existing algorithms for solving DSBs have so far failed to utilize the structure of aligned data, which naturally arises in many biological phenomena. In this paper, we propose a novel algorithmic framework that, for the first time, solves DSBs while respecting the data alignment. Our approach hinges on a combination of two decades-old ideas: The classical Schrödinger bridge theory and Doob’s h-transform. Compared to prior methods, our approach leads to a simpler training procedure with lower variance, which we further augment with principled regularization schemes. This ultimately leads to sizeable improvements across experiments on synthetic and real data, including the tasks of protein conformational changes and temporal evolution of cellular differentiation processes.</p>
Alignments used for phylogenetic analysis of capirona (Calycophyllum spruceanum, Rubiaceae)
<p>Capirona (<em>Calycophyllum spruceanum</em> Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree, with origin in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct librar-ies. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of <em>C. spruceanum</em> cp genome predicted 87 protein-coding genes (CDS), eight ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotide (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than invert regions. Finally, phylogenetic analysis resolved that C. spruceanum is a sister species to Emmenopterys henryi, and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of <em>C. spruceanum</em>, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.</p>
An Empirical Model for Mercury's Field-Aligned Currents Derived from MESSENGER Magnetometer Data
<p>Companion dataset for manuscript titled "An Empirical Model for Mercury’s Field-Aligned Currents Derived from MESSENGER Magnetometer Data" submitted to <em>JGR: Space Physics</em>.</p> <p>The file MESSENGER_MAG_Disturbance_Indices_v12.txt defines the Mercury disturbance index as a function of MESSENGER orbit number.</p> <p>The file rsuns.txt defines the Mercury’s Heliocentric distance as a function of time.</p> <p>The file merge_magrdr_11083_15120_actidx_kt17res.txt contain the processed MESSENGER magnetometer vectors. This file is further broken into quintiles based on the disturbance index.</p>
A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction
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Alignment underpinning the molecular phylogeny of the Streptophyta based on SSU rDNA and rbcL sequence comparisons presented in Figure S1 of the article "Phylogenomic insights into the first multicellular streptophyte"
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Primer Aligner Study
ClinicalTrials.gov study NCT02550938. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Muscle Property, Alignment and Joint Loading in People With Knee Osteoarthritis
ClinicalTrials.gov study NCT03628508. IPD Sharing: NO. Countries: 1. Publications: 0.
Comparison of Alignment Achieved Using the VELYS Robotic-Assisted Solution Versus Manual Instrumentation in Total Knee Arthroplasty
ClinicalTrials.gov study NCT04730271. IPD Sharing: YES. Countries: 1. Publications: 0.
Assessment of Foot Alignment and Pressure After Correction of Varus Knee by High Tibial Osteotomy or Total Knee Replacement
ClinicalTrials.gov study NCT05314972. IPD Sharing: Not stated. Countries: 0. Publications: 8.
Alignment Comparison Between TruMatch™ Personalized Solutions and Conventional Total Knee Replacement Instrumentation
ClinicalTrials.gov study NCT01108237. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Patient Aligned Care Team (PACT) Intensive Management (PIM) Project
ClinicalTrials.gov study NCT03100526. IPD Sharing: NO. Countries: 0. Publications: 2.
Pelvic Alignment and Shoulder Function
ClinicalTrials.gov study NCT03022305. IPD Sharing: NO. Countries: 0. Publications: 4.
Accuracy of Dental Movements Using Clear Aligners Treatment: a Single-center Prospective Observational Study
ClinicalTrials.gov study NCT06561945. IPD Sharing: NO. Countries: 0. Publications: 5.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.