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32 results for “structure alignments”
Cross-phyla protein annotation by structural prediction and alignment
<p><strong>Background:</strong> Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer protein identity, however this approach loses predictive power at longer evolutionary distances. Here we propose a workflow for protein annotation using structural similarity, exploiting the fact that similar protein structures often reflect homology and are more conserved than protein sequences.</p> <p><strong>Results:</strong> We propose a workflow of openly available tools for the functional annotation of proteins via structural similarity (MorF: <strong>Mor</strong>pholog<strong>F</strong>inder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in >90% cases, and annotates an additional 50% of the proteome beyond standard sequence-based methods. We uncover new functions for sponge cell types, including extensive FGF, TGF and Ephrin signalling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls.</p> <p><strong>Conclusions:</strong> Our work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this to be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.</p>
Datasets of sequences, alignments and structural models generated for the structural prediction of complexes mediated by intrinsically disordered regions.
<p>This repository contains input and ouput files used and generated for the scanning of intrinsically disordered region and the prediction of their binding sites to receptor proteins using the <a href="https://github.com/i2bc/SCAN_IDR">SCAN_IDR</a> pipeline with AlphaFold2-Multimer.</p><p>It contains two archives: </p><ol><li><a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> dedicated to the analysis of a dataset of 42 protein complexes non redundant with the dataset used for AlphaFold2 training,</li><li><a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> dedicated to the analysis of 923 complexes from the ELM database.</li></ol><p>These data can be used to rerun specific sections of the pipeline and scripts provided in: <a href="https://github.com/i2bc/SCAN_IDR">https://github.com/i2bc/SCAN_IDR</a></p><h4><strong>Dataset of 42 non redundant complexes</strong></h4><p>The first archive <a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> contains 3 compressed directories and a README file detailing their contents :</p><ul><li>the initial raw sequence and alignment data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the input and output data of every Alphafold run for every complex -> DIRECTORY <strong>af2_runs/</strong></li><li>the native reference structures -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p>The protein-peptide complex cases have been assigned a distinct index number, from 1 to 42, consistent across the several directories of the archive. Their corresponding directories are labelled as <i><index>_<pdbcode></i>.</p><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.2</i></p><h4><strong>Dataset of 923 complexes selected from the ELM database</strong></h4><p>The second archive <a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> contains input and ouput files used and generated for the analysis of 923 Eukaryotic Linear Motifs (ELM) database entries.</p><p>Each ELM entry is indexed with specific integer id and is composed of a receptor and a ligand protein. </p><p>The archive contains a Table associating ELM indexes with the ELM entry information, 5 directories and a README file detailing their contents:</p><ul><li>the table describing ELM entries -> FILE <strong>Table_923ELM_uid_delimitations_info_for_archive.txt</strong></li><li>the initial raw sequence and multiple sequence alignment (MSA) data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the concatenated MSA model for every ELM complex and protocol used -> DIRECTORY <strong>af2_elm_coali_inputs/</strong></li><li>the best model of every AF2 protocol for every complex according to the AF2 -> DIRECTORY <strong>af2_elm_models/</strong></li><li>the best model cut in the ligand part to select only the ELM motifs as used for the evaluation of the models -> DIRECTORY <strong>elm_cut_models/</strong></li><li>the reference structures used for the evaluation of the models -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.3</i></p>
Data description: Deprivation of loading during early healing of rat Achilles tendons affects extracellular matrix composition and structure, and reduces cell density and cell alignment
<p><a name="_Hlk158643946"></a><strong>Data description: Deprivation of loading during early healing of rat Achilles tendons affects extracellular matrix composition and structure, and reduces cell density and cell alignment</strong></p> <p><em>Malin Hammerman, Maria Pierantoni, Hanna Isaksson<sup> *</sup>, Pernilla Eliasson <sup>*</sup></em></p> <p><em><sup>* </sup></em><em>joint<sup> </sup>last authors</em></p> <p>This dataset contains microscope images obtained from sections of healing and intact rat Achilles tendons undergoing different in vivo loading protocols and different time points post-transection. The data presented are the full resolution microscope images available in lower resolution in the accompanying manuscript’s Supplementary Figures 4-6.</p> <p>Each zipped folders contain images (tif-files) from all time-points for each respective staining and loading group. </p> <ul> <li>Col1: Sections stained with Collagen 1 antibodies</li> <li>Col3: Sections stained with Collagen 3 antibodies</li> <li>Elastin: Sections stained with Elastin antibodies</li> <li>Full_loading: Free cage activity</li> <li>Reduced_loading: Paralysis of the calf muscle with Botox</li> <li>Minimal_loading: Botox combined with joint fixation using a steel-orthosis</li> <li>Intact_reference: Contralateral uninjured Achilles tendons, used as reference</li> </ul> <p>More description of the datasets inside the zipped files are available below and in the file 'Data Description.pdf'</p> <p> </p> <p><strong>Brief re-cap of methods</strong></p> <p>Histological analysis was performed on healing Achilles tendons from Female Sprague-Dawley rats, specific-pathogen free (11-12 weeks, weight 299 ± 15 g), that had undergone full transection [13] of the right Achilles tendon, and been exposed to different levels of loading. Altered loading was imposed through two mechanisms. Reduced loading involved intramuscular Botox injections in the right calf muscles to induce plantar flexor muscle paralysis [24]. Additionally, the rats in the minimal loading group received a steel-orthosis around their right hindlimb directly after surgery [24].</p> <p>Snap frozen tendons in OCT were sectioned longitudinally (7 μm thickness) and stained with immunofluorescent staining for collagen 1, collagen 3, or elastin. Sections were counterstained with DAPI followed by mounting. The tissue sections were imaged under a microscope (DMi8, Leica Microsystems, Wetzlar, Germany, with a Hamamatsu Orca LT Flash sCMOS camera) where fluorescence was detected at 550 nm (secondary antibody Alexa Fluor 594), 470 nm (secondary antibody Alexa Fluor 488) and 385 nm (DAPI), and exposure time was held constant for each color channel regarding magnification and staining.</p> <p>Mapping images of the entire tendon were obtained for one section per group (n=1 per healing time, loading group and ECM matrix protein). All images were adjusted to the negative control, where the primary antibody was omitted, to correct for unspecific antibody detection.</p> <p><strong>Microscope images and description of file-names </strong></p> <p>All data is presented in the form of .tif files. Please refer to the scale bars in the images. All image-files are named using the following abbreviations, as described below. As an example, the file name “Tendon_col1_FL_1W_col1.tif” refers to a tendon section stained for collagen 1 from a rat exposed to full loading for a period of 1 week after tendon transection, where only the channel for collagen 1 is shown, whereas “Tendon_col1_FL_1W_merged.tif” includes the channels for both staining for collagen 1 and DAPI of the same section.</p> <p>Col1: Sections stained with Collagen 1 antibodies<br>Col3: Sections stained with Collagen 3 antibodies<br>Elastin: Sections stained with Elastin antibodies<br>dapi: Sections stained with 4',6-Diamidino-2-Phenylindole Dihydrochloride.<br>FL: Full loading (free cage activity),<br>RL: Reduced loading (paralysis of the calf muscle with Botox),<br>ML: Minimal loading (Botox combined with joint fixation using a steel-orthosis)<br>IT: Intact contralateral Achilles tendons, used as reference.</p> <p>1W: Healing time point 1 week after transection<br>2W: Healing time point 2 weeks after transection<br>3W: Healing time point 3 weeks after transection<br>20W: Healing time point 20 weeks after transection</p> <p><strong>Settings for brightness and contrast</strong></p> <p><em>Collagen 1</em><br>1w FL 2000-12 000, UL 4000-10 000, ML 4000-12 000<br>2w FL 2500-10 000, UL 4000-10 000, ML 5000-12 000<br>3w FL 2000-12 000, UL 3500-13 000, ML 3500-14 000<br>12w FL 3000-12 000<br>20w FL 3000-11 000<br>IT 2000-8 000</p> <p>Collagen 3<br>1w FL 3000-12 000, UL 4000-10 000, ML 4000-13 000<br>2w FL 2000 - 7 000, UL 2500-12 000, ML 2000-12 000<br>3w FL 2000-12 000, UL 3500-13 000, ML 3500-14 000<br>12w FL 3000-12 000<br>20w FL 2000-12 000<br>IT 3000-12 000</p> <p>Elastin<br>1w FL 4000-10 000, UL 5000 - 8000, ML 3500-12 000<br>2w FL 3000-12 000, UL 3000-12 000, ML 3000-12 000<br>3w FL 2500-12 000, UL 2000-12 000, ML 2500-12 000,<br>12w FL 3500-12 000<br>20w FL 3500-12 000<br>IT 2000-12 000</p>
Polymerase Structure Alignments - v4 Update (July 2022)
<p>v4 update (July 2022) of superposed viral polymerase structures using the methodology described in <br> <em>A Comprehensive Superposition of Viral Polymerase Structures</em> by Olve Peersen, <a href="https://www.mdpi.com/1999-4915/11/8/745">Viruses 2019 11(8) 745</a>.</p> <p> • <strong>_All_PDBs_v4.zip</strong> contains a single directory with coordinate files for 917 structures taken from 628 PDB entries. Uncompressed size is 1.6 GB.</p> <p> • <strong>Polymerases_v4.zip</strong> contains the complete set of files from the superpositions, including the _All_PDBs/ directory. Uncompressed size is 5.7 GB.</p> <p>---------------------------------------------------------------------------------------------------------------<br> POLYMERASE STRUCTURES community page at Zenodo.org </p> <p> v4 Release July 19, 2022</p> <p> 917 structures from 628 PDB entries</p> <p> http://www.zenodo.org/communities/pols/ <br> =========================================================================================</p> <p>This directory contains a large collection viral polymerase structure coordinates that have been superposed using the methods described in Peersen, Viruses 2019, 11(8), 745. </p> <p>They are released into the public domain under the Creative Commons Attribution (CC BY) license. </p> <p>Please cite the following two references for any derivative work:</p> <p> 1) Reference to the publication describing the methodology:<br> Peersen, OB<br> A Comprehensive Superposition of Viral Polymerase Structures.<br> Viruses 2019, 11(8), 745 <br> https://doi.org/10.3390/v11080745</p> <p> 2) DOI reference that always resolves to the latest release of the dataset:<br> Peersen, OB<br> Polymerase Structure Alignments<br> https://doi.org/10.5281/zenodo.3361874</p> <p><br> ---------------------------------------------------------------------------------------------<br> Olve Peersen Olve.Peersen@ColoState.edu<br> Professor<br> Biochemistry & Molecular Biology<br> 1870 Campus Delivery<br> Colorado State University<br> Ft. Collins, CO 80523-1870<br> -------------------------------------------------------------------------</p> <p>=============================================================================</p> <p>v4 220719 - Many updates and several news sets, as outlined below. <br> The total count is now 917 polymerase structures from 628 PDB entries</p> <p> 2-rddp: Foamyvirus FOAM added, but rest of set left unchanged</p> <p> 3-dsdn: Simplified as hsv1 was pulled into its own set (see below)</p> <p><br> NEW alph: Alphaviruses - RRV: 7f0s,<br> SINV: 7vb4, 7vw5</p> <p> aren: Lassa: 7ckl, 7ela, 7och, 7oe3, 7oe7, 7oea, 7oeb,<br> 7ojj, 7ojk, 70jl, 7ojn<br> Machupo: 7ckm, 7el9, 7elb, 7elc, 7vgq, 7vh1, 7vh2, 7vh3</p> <p> buny: RVF: 7eei<br> LaCrosse: 7ori, 7orj, 7ork, 7orl, 7orm, 7orn, 7oro</p> <p> coro: 7dfg, 7dfh, 7doi, 7dok, 7dte, 7ed5, 7egq, 7eiz, 7krn, 7kro, 7krp, <br> 7oyg, 7ozu, 7ozv, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 7thm </p> <p> fluv: 7nha, 7nhc, 7nhx, 7ni0, 7nik, 7nil, 7nir, 7nis, 7nj3, 7nj4, 7nj5, <br> 7nj7, 7nk1, 7nk2, 7nk4, 7nk6, 7nk8, 7nka, 7nkc, 7nki, 7nkr, 7z42, <br> 7z43, 7z43, 7z4o, 7z4o</p> <p> NEW foam: Foamyviruses - 7o0g, 7o0h, 7024<br> Created FOAM.pdb from core of 7o0g.pdb, which was <br> superposed on rddp set, but the orientations of other <br> members of that set (HIV,MMLV,TERT) were not updated.</p> <p> NEW hsv1: Herpes Simplex Virus - 2gv9, 7luf</p> <p> pest: Classic Swine Fever Virus: 7ekj</p> <p> poxv: 7amv, 7aof, 7aoh, 7aoz, 7ap8, 7ap9</p> <p> rb69: 2atq, 7f4y</p> <p> tavp: 7om2, 7om6, 7om7, 7om9, 7oma<br> </p>
Supplementary materials for "Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments"
<p>Supplementary materials for "Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments". These include precalculated RNA Blocks, MBRs (Matrix of Bear encoded RNA), sPSSMs (structural Position Specific Scoring Matrix), RIG (Relative Information Gain) scores, and plots calculated for 3016 Rfam 14.1 families. In particular:</p> <ul> <li><strong>alignments.zip:</strong> zipped file containing the structural alignments for each Rfam family.</li> <li><strong>RNA_Blocks.zip</strong>: zipped file containing the RNA blocks used to derive different substitution matrices.</li> <li><strong>MBRs.zip</strong>: zipped file containing the substitution matrices.</li> <li><strong>sPSSMs.zip</strong>: zipped file containing the structural Position Specific Scoring Matrices.</li> <li><strong>RIGs.zip</strong>: zipped file containing the RIG scores.</li> <li><strong>entropy.zip</strong>: zipped file containing the (rescaled) entropy.</li> <li><strong>plots.zip</strong>: zipped file containing the plots. </li> </ul> <p>All the scripts to build all these files are available at <a href="https://github.com/helmercitterich-lab/RIG">https://github.com/helmercitterich-lab/RIG</a>.</p>
Underlying data for "Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms"
<p><strong>Output Files from Structural Alignment of TRP Channels</strong><br> The archive contains the key output files resulting from the structural alignment of members of the TRP channel family described in "Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms", Huffer et al., (2020), eLife.</p> <p><strong>Contents of trp_struct_align_outputs.tar.gz</strong><br> <em>Aligned_structures</em><br> For each alignment where the transmembrane (TM) domain of the mobile structure was aligned to the TM domain of the stationary/reference structure (6co7):<br> 1) mobile_stationary_full_align.pdb: aligned based on Fr-TM-Align output matrix, contains all residues<br> 2) mobile_stationary_tmem_align.pdb: aligned based on Fr-TM-Align output matrix, contains only TM residues used for alignment<br> 3) mobile_stationary_hole.pdb: aligned based on Fr-TM-Align output matrix, contains HOLE profile of mobile structure</p> <p><em>Alignments</em><br> Multiple sequence alignments constructed using the TM domain of each structure as the stationary/reference structure, with all other structures aligned pairwise.<br> 1) stationary_full.ali: Full multiple sequence alignment containing all TM residues from all stationary and mobile structures.<br> 2) stationary_nogap.ali: Multiple sequence alignment containing all TM residues from the stationary structure. Any gaps in the stationary structure removed, which removes any residue in any mobile structure that does not align to the stationary/reference structure.</p> <p><em>Fr-TM-Align_outputs</em><br> - frtmalign_output.csv: contains all information from Fr-TM-Align output files for each pairwise alignment of TM domains, including PDB IDs of mobile and stationary structures, lengths of mobile and stationary structures, length of pairwise alignment sequence, RMSD of alignment, TM-score of alignment, and sequence identity of alignment.<br> - aligned_length.csv, RMSD.csv, sequence_identity.csv, and TM_score.csv: csv files containing the specified values for all pairwise alignments of TM domains, with the mobile structure in rows and stationary structure in columns</p> <p><strong>Reproducibility</strong><br> Code to reproduce this alignment and analysis is available on GitHub at: <a href="https://github.com/kehuffer/TRP_Structural_Alignment">https://github.com/kehuffer/TRP_Structural_Alignment</a></p>
Improving phonetic alignment by handling secondary sequence structures
<p>Supplementary material accompanying the paper "Improving phonetic alignment by handling secondary sequence structures".</p> <p>The data consists of 5 files:</p> <ul> <li>gold_standard.psa : the gold standard used in the analysis in PSA format</li> <li> sca-secondary.psa : the output of the algorithm with the secondary extension</li> <li>sca-traditional.psa : the output of the traditional algorithm</li> <li>sca-secondary-diff.psa : the differences of the secondary extension compared to the GS</li> <li>sca-traditional-diff.psa : the differences of the traditional algorithm compared to the GS</li> </ul> <p>For a description of the file-format used in this dataset, please refer to the LingPy tutorial under http://lingpy.org.</p>
Flash propagation and inferred charge structure relative to radar-observed ice alignment signatures in a small Florida Mesoscale Convective System
<p>Data for paper of above title, submitted to <em>Geophysical Research Letters</em>, June 2017. Manuscript number: 2017GL072767</p>
Utilizing Hydrothermal Processing to Align Structure and In Vitro Digestion Kinetics between Three Different Pulse Types
<p>The data used for the graphs in the paper: Pälchen, K.; Van den Wouwer, B.; Duijsens, D.; Hendrickx, M.E.; Van Loey, A.; Grauwet, T. Utilizing Hydrothermal Processing to Align Structure and In Vitro Digestion Kinetics between Three Different Pulse Types. <em>Foods </em><strong>2021</strong>, <em>11</em>, 206. https://doi.org/10.3390/foods11020206</p> <p><strong>Abstract</strong></p> <p>Processing results in the transformation of pulses’ structural architecture. Consequently, digestion is anticipated to emerge from the combined effect of intrinsic (matrix-dependent) and extrinsic (processed-induced) factors. In this work, we aimed to investigate the interrelated effect of intrinsic and extrinsic factors on pulses’ structural architecture and resulting digestive consequences. Three commercially relevant pulses (chickpea, pea, black bean) were selected based on reported differences in macronutrient and cell wall composition. Starch and protein digestion kinetics of hydrothermally processed whole pulses were assessed along with microstructural and physicochemical characteristics and compared to the digestion behavior of individual cotyledon cells isolated thereof. Despite different rates of hardness decay upon hydrothermal processing, the pulses reached similar residual hardness values (40 N). Aligning the pulses at the level of this macrostructural property translated into similar microstructural characteristics after mechanical disintegration (isolated cotyledon cells) with comparable yields of cotyledon cells for all pulses (41–62%). We observed that processing to equivalent microstructural properties resulted in similar starch and protein digestion kinetics, regardless of the pulse type and (prolonged) processing times. This demonstrated the capacity of (residual) hardness as a food structuring parameter in pulses. Furthermore, we illustrated that the digestive behavior of isolated cotyledon cells was representative of the digestion behavior of corresponding whole pulses, opening up perspectives for the incorporation of complete hydrothermally processed pulses as food ingredients.</p>
Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectral Alignment For Discovery of Structurally Related Molecules
<p>Spectral libraries and analysis results of the evaluation between the cosine similarity, modified cosine similarity, and neutral loss matching for the discovery of structurally related molecules.</p> <p>Spectral libraries used as input:<br> - MassIVE-KB peptide spectral library (version 2018/06/15): LIBRARY_CREATION_AUGMENT_LIBRARY_TEST-82c0124b-download_filtered_mgf_library-main.mgf<br> - GNPS community spectral libraries (downloaded on 2022/05/12): ALL_GNPS_NO_PROPOGATED.mgf<br> - GNPS bile acids spectral library (downloaded on 2022/05/12): BILELIB19.mgf</p> <p>Analysis output results:<br> - massivekb_peptide_mods.csv: 955,228 peptide MS/MS spectrum pairs from MassIVE-KB<br> - gnps_libraries.csv: 10 million small molecule MS/MS spectrum pairs from the GNPS community spectral libraries<br> - gnps_libraries_metadata.csv: structural (InChI, SMILES) and class information (computed using Classyfire) for 58,165 small molecule spectra from the GNPS community spectral libraries<br> - gnps_bilelib.csv: 340,637 bile acids MS/MS spectrum pairs from the GNPS bile acids spectral library</p> <p>For more information, see: https://github.com/bittremieux/cosine_neutral_loss/</p>
Data file with manuscript titled 'A Structurally Validated Sequence Alignment of 497 Human Protein Kinase Domains'
<p>The files used in different analysis reported in the manuscript titled - 'A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains' are shared at two locations. Following is a brief description of these files.</p> <p>Location - https://github.com/DunbrackLab/Kinases<br> 1. HMM profile files - HMM files for each of the nine groups computed separately labeled as Groupname.hmm, like AGC.hmm<br> 2. HMM profile file - HMM file computed from the full alignment including all the sequences - Human-PK.hmm<br> 3. Score files - HMM scores of each kinase sequence against all the groupwise HMMs both for iteration1 (HMM-iter1-scores-tables.txt) and iteration2 (HMM-iter1-scores-tables.txt)<br> 4. Jalview session file - Kinase alignment with sequences colored by secondary structure information from PDB file if the structure is known; or predicted secondary structure if the experimental structure is not known. The file could be opened in Jalview - kinases-PDB-SSPred.jvp</p> <p>Location - https://zenodo.org/record/3445533<br> 1. The file contains list of residue pairs aligned in pairwise structural alignments of 272 human protein kinases which were used as a benchmark in the study. The alignments were created by FATCAT and optimized by SE program.</p>
Repository for the Method Article "Oriented artificial nanofibers and laser induced periodic surface structures as substrates for Schwann cells alignment"
<p>Repository containg the underlaying and extended data for the paper "Oriented artificial nanofibers and laser induced periodic surface structures as substrates for Schwann cells alignment".</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>
Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis
This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ∼33 of the ∼36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/≃jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A–F, or 6A–C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly divergent cephalopod and urochordate sequences out of those clades. Unlikely to be correct, these refutations show for the first time that rRNA phylogeny can support some 'wrong' clades. Along with its weaknesses, the rRNA tree has strengths: It recovers many clades that are supported by independent evidence (e.g., Metazoa, Bilateria, Hexapoda, Nonoculata, Ambulacraria, Syndermata, and Thecostraca with Malacostraca) and shows good resolution within certain groups (e.g., in Platyhelminthes, Insecta, Cnidaria). As another strength, the newly added rRNA sequences yielded the first rRNA-based support for Carnivora and Cetartiodactyla (dolphin + llama) in Mammalia, for basic subdivisions of Bryozoa ('Gymnolaemata + Stenolaemata' versus Phylactolaemata), and for Oligostraca (ostracods + branchiurans + pentastomids + mystacocarids). Future improvement could come from better sequence-evolution models that account for base-compositional heterogeneity, and from combining rRNA with protein-coding genes in phylogenetic reconstruction.
Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone
<p>Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to <em>Haliotis virginea</em> Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: 1) the Three Kings Islands; 2) the Auckland, Chatham and Antipodes Islands; and 3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our non-reliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.</p>
Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data
<p>Source data for the paper "Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data"</p>
Evaluate Cytotoxicity, Leaching, and Structural Conformation of Clear Aligners
ClinicalTrials.gov study NCT06503029. IPD Sharing: NO. Countries: 1. Publications: 4.
Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis
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Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone
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Protein structure alignments and structural similarity score code for: Benchmarking methods of protein structure alignment
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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.