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This repository contains genome annotation files for the genome assembly reported in Kapheim et al. 2020.
Data Types:
  • Other
  • Sequencing Data
  • Tabular Data
  • Dataset
System: POPC membrane with 72 (36 x 36) lipids Number of POPC: 72 Number of Waters: 2520 Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Force Field: CHARMM36 Simulation engine: NAMD Git-2020-02-27 for Linux-x86_64-multicore-CUDA [Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)] Number of independent repeats per setup: 1. Trajectory lengths per repeat: 100 ns. Previously equilibrated for: 0 ns. Sampling rate: every 100 ps. Time integration step: 2 fs. (For further info, please see the .inp file)
Data Types:
  • Other
  • Software/Code
  • Geospatial Data
  • Sequencing Data
  • Dataset
Tutorial data for chloroplast genome assembly: fastq reads from illumina and nanopore sequencing for the sweet potato. Data from: Zhou C, Duarte T, Silvestre R et al. 2018 (https://doi.org/10.12688/gatesopenres.12856.1), hosted at EBI ENA under accession numbers: illumina (SRR6828568) and nanopore (SRR6828567). This is how the files have been changed from the original datasets: illumina-reduced: has the first 62,500 reads only illumina-tiny: has the first 12,500 reads only nanopore-reduced: has the first 2,000 reads only nanopore-tiny: has the first 250 reads only
Data Types:
  • Sequencing Data
  • Dataset
Data for an examplary metaproteomics data analysis with the MetaProteomeAnalyzer (MPA) and Prophane software tools. Data is from the PRIDE dataset PXD010550. Files include: protein databases (FASTA) : UniProt Swiss-Prot: UniprotSwP-2020_03.fasta Metagenome (+ Swiss-Prot): MG_BG__UPSP.fasta MS Datasets (MGF): FASP digest: FASP_BGP_A.mgf In-gel digest: InGel_BGP_A.mgf Example results for a single experiment analysis (Sample A, based on: MS data: FASP digest, FASTA: UniProt Swiss-Prot): MPA results: mpa_result-sample_a-fdr_0.05-single_exp.csv Prophane results: prophane_result-sample_a.zip Example results for a multi-experiment analysis (Sample B, based on: MS data: FASP + in-gel digest, FASTA: Metagenome): MPA results: mpa_result-sample_b-fdr_0.01-multi_exp.csv Prophane results: prophane_result-sample_b.zip MPA data dump including preprocessed UniProt Swiss-Prot FASTA (optionally used by conda mpa-server package)
Data Types:
  • Software/Code
  • Sequencing Data
  • Tabular Data
  • Dataset
  • File Set
Data for an examplary metaproteomics data analysis with the MetaProteomeAnalyzer (MPA) and Prophane software tools. Data is from the PRIDE dataset PXD010550. Files include: protein databases (FASTA) : UniProt Swiss-Prot: UniprotSwP-2020_03.fasta Metagenome (+ Swiss-Prot): MG_BG__UPSP.fasta MS Datasets (MGF): FASP digetst: FASP_BGP_A.mgf in get digest: InGel_BGP_A.mgf MPA data dump including preprocessed UniProt Swiss-Prot FASTA (optionally used by conda mpa-server package)
Data Types:
  • Software/Code
  • Sequencing Data
  • Dataset
  • File Set
LSU, SSU and ITS rDNA sequence alignments for the description of two new toxic species of Gambierdiscus, G. holmesii and G. lewisii, on which phylogenetic inferences were based.
Data Types:
  • Sequencing Data
  • Document
Symbiodiniaceae DNA sequences and community datasets
Data Types:
  • Sequencing Data
  • Tabular Data
  • Dataset
Additional file 12 of the publication "ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms". Each PDB file describes the docking of wt/expanded ATXN1 with an interactor.
Data Types:
  • Sequencing Data
  • Dataset
This archive contains generation files and homology models of human annexin A11’s C-terminal domain (residues 192-505) with or without 4 bound calcium ions, built using human annexin A4 with bound calcium. Representative models A single representative model was selected for the apo: anxa11_cterm.B99990009.pdb A single representative model was selected for the holo protein: anxa11_cterm.B999900038.pdb Methods The template coordinates of chain A were extracted from PDB ID 2ZOC. The alignment contains no gaps, as indicated by iTasser. In the holo model, distance restraints between calcium ions and nearby oxygen atoms were assigned based on the equivalent distances in the template, as computed using PyMol. The final model was selected from the attached ensemble of 100 models in the *all_100_models* folder. Models were generated by Modeller 9.20 with the input files in the *Modeller_files/* subfolder, before filtration with MolPDF, then ProQ, then PROCHECK, then MolProbity. Electrostatic surfaces were shown using the files in the *Electrostatics/* subfolder. The calcium atoms were renamed using *rename_cal.csh*, and the resultant pdb file *anxa11_cterm.B99990038_rename.pdb* was used as input to generate the correct partial charges using APBS v1.3 with the CHARMM force field. The maps of the calcium-free model were generated for the pdb file *anxa11_cterm.B99990009.pdb*. This assumes no major conformational changes occur as a result of calcium binding, which is likely to be the case, based on comparison of calcium-bound 2ZOC and calcium-free 2ZHJ. The pymol session containing the maps can be viewed with Pymol v2.3.0 This work was supported by the National Institutes of Health, National Institute of Neurological Disorders and Stroke intramural research program. For more details, see Liao Y-C, Fernandopulle M, Wang G, Choi H, Hao L, Drerup CM, Qamar S, Nixon-Abel J, Shen Y, Meadows W, Vendruscolo M, Knowles T, Nelson M, Czekalska M, Musteikyte G, Gachechiladze M, Patel R, Stephens C, Pasolli A, Forrest LR, St George-Hyslop P, Lippincott-Schwartz J, Ward ME, "RNA granules hitchhike on lysosomes for long-distance transport, using annexin A11 as a molecular tether" Cell (2019) in press.
Data Types:
  • Other
  • Sequencing Data
  • Text
  • File Set
Patients sequences dataset from the study "Hepatitis C virus (HCV) genotype 1 displays higher genetic variability of hypervariable region 1 (HVR1) than genotype 3" . They consist of error-corrected and reconstructed intra-host HVR1 genetic populations.
Data Types:
  • Sequencing Data
  • Document