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47 results for “structural annotation”
FIGURE 8 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 8. Cluster analysis of habitat types at the Laje de Santos Marine State Park based on the similarity of species composition. The relative distribution of trophic categories in each habitat is shown in the graphs. CAR = Carnivore; MIF = Mobile Invertebrate Feeder; OMN = Omnivore; PIS = Piscivore; PLK = Planktivore; ROVH = Roving Herbivore; SIF = Sessile Invertebrate Feeder; TERH = Territorial Herbivore.
FIGURE 10 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 10. Targeted and endangered top-predators recorded at the Laje de Santos Marine State Park. The dusky groupers Mycteroperca marginata are very common in the area, but attain unusual large size and are largely unafraid of divers, contrarily to what happens at other unprotected sites (a); the goliath grouper Epinephelus itajara (b) and the cubera snapper Lutjanus cyanopterus (c). Several individuals of these two latter species have been seen at in the Laje de Santos in the last two years, after a period of more than ten years over which they remained unrecorded at the site. Photos: A. Carvalho-Filho (c); L. Cheidde (b); A. Valente (a).
FIGURE 3 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 3. Some abundant fish species at the Laje de Santos Marine State Park. The tomtate grunt Haemulon aurolineatum (a); adult and juvenile sergeant major Abudefduf saxatilis (b); the brown chromis Chromis multilineata (c); juvenile dusky damselfish Stegastes fuscus (d); intermediate individual of the jubauna reeffish Chromis jubauna (e); the silver porgy Diplodus argenteus (f); juvenile porkfish Anisotremus virginicus (g); the ringneck blenny Parablennius pilicornis (h). Photos: O.J. Luiz Jr, except (e) by L.F. Cassino.
FIGURE 6 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 6. Selected fish species that dwell in the deep reef (30-45 m) community at the Laje de Santos State Marine Park. The deep-reef wrasse Halichoeres sp.n. (a); the reeffish Chromis cf. enchrysura (b); the red porgy Pagrus pagrus (c); the Brazilian sandperch Pinguipes brasilianus (d); the sea basses Acanthistius brasilianus (e), A. patachonicus (f) and Dules auriga (g); the snowy grouper Hyporthodus niveatus (h). The former species (a) is probably a Brazilian endemic, closely related to the Northwestern Atlantic species H. bathyphilus. The distinctive status from its sister species is supported by molecular mtDNA analysis (L.A. Rocha pers. comm.).The last six species (c-h) ranges southward to temperate Patagonian rocky reefs. Photos: A. Carvalho-Filho (e-g); O.J. Luiz Jr. (a-d, h).
FIGURE 4 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 4. Relative proportions of geographic distribution types of the species observed at the Laje de Santos Marine State Park. Br = Brazilian Province; CE = Central Atlantic; CT = Circumtropical. EA = Eastern Atlantic; SCa = Southern Caribbean; SE = Southeastern Brazil; TA = Trans-Atlantic; WA = Western Atlantic.
FIGURE 5 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 5. Selected Brazilian endemic reef fish species that occur at the Laje de Santos Marine State Park. The barber goby Elacatinus figaro (a); the Brazilian yellowcheek wrasse Halichoeres dimidiatus, initial phase (b); the Brazilian wrasse Halichoeres brasiliensis, intermediate phase (c); the Noronha wrasse Thalassoma noronhanum, terminal male (d); the tuiupiranga parrotfish Sparisoma tuiupiranga, initial phase (e); Zelinda's parrotfish Scarus zelindae, initial phase (f); the reef parrotfish Sparisoma amplum, initial phase (g); the gray parrotfish Sparisoma axillare, terminal male (h). Photos: O.J. Luiz Jr, except (d) by I. Cavas.
Energy and forces annotated atomic structures of platinum using first-principles calculations
<p>Dataset for training machine learning potential of platinum.</p> <p>Detailed explanation of data generation is described in the preprint. below</p> <p>Chun, H., Kang, J., Kang, D., Heo, J., Cho, H., Heo, J., … & Han, B. (2022). Tracking the 3d atomic structures during thermal treatment and catalytic activity of individual pt nanoparticles.. https://doi.org/10.21203/rs.3.rs-1441062/v1</p>
DomainMapper: Accurate Domain Structure Annotation Including Those with Non-contiguous Topologies
<p>List of Uniprot proteomes used in the study "DomainMapper: Accurate Domain Structure Annotation Including Those with Non-contiguous Topologies"</p> <p>Contains the following proteomes:</p> <p>Aug 9 2021 H. spaiens - uniprot-proteome_UP000005640.fasta</p> <p>Aug 9 2021 D. melanogaster - uniprot-proteome_UP000000803.fasta</p> <p>Aug 9 2021 E. coli - uniprot-proteome_UP000000625.fasta</p> <p>Aug 9 2021 M. musculus - uniprot-proteome_UP000000589.fasta</p> <p>Aug 9 2021 S. cerevisiae - uniprot-proteome_UP000002311.fasta</p> <p>Nov 1 2021 S. aureus - uniprot-proteome_UP000008816.fasta</p> <p>Nov 1 2021 Z. mays - uniprot-proteome_UP000007305.fasta</p> <p>Jul 28 2022 M. jannaschii - uniprot-proteome_UP000000805.fasta</p>
The gene structure annotation, gene function annotation and TE annatition files of the Glyphodes pyloalis's genome
Open the record for dataset details and reuse information.
The gene structure annotation, gene function annotation and TE annatition files for the Cibotium barometz isolate CiBa-2024 genome
<p>This dataset comprises comprehensive annotation files for the genome of Cibotium barometz (Golden Chicken Fern), isolate CiBa-2024. It includes gene structure predictions, functional annotations, and transposable element (TE) identifications, complementing the chromosome-level genome assembly. The gene structure annotation provides detailed information on predicted gene models, including exon-intron boundaries and coding sequences. Functional annotations offer insights into the potential roles of identified genes, including Gene Ontology (GO) terms, protein domains, and pathway associations. The TE annotation file details the classification and distribution of transposable elements within the genome. These annotations were generated using state-of-the-art bioinformatics tools and databases, offering a valuable resource for researchers studying fern genomics, plant evolution, and the genetic basis of C. barometz's unique biological features, including its medicinal properties. This dataset aims to facilitate further research in comparative genomics, functional studies, and the exploration of fern biology and evolution.</p>
Figs. 10–14. Morphological structures. 10 in Larval Psephenidae (Coleoptera: Byrrhoidea) of Thailand:Annotated List and Illustrated Key to Genera
Figs. 10–14. Morphological structures. 10) Schinostethus: Gills concealed beneath ventral operculum; 11) Undescribed Eubrianacinae: Palmate gills exposed on venter; 12) Psephenoidinae: Ninth abdominal segment surrounded by paratergites of eighth abdominal segment; 13) Schinostethus: Ninth abdominal segment not surrounded by paratergites of eighth abdominal segment; 14) Mataeopsephus: Gills with branches arising from central stalk. 7 = seventh abdominal segment; 8 = eighth abdominal segment; 9 = ninth abdominal segment.
Figs. 15–20. Morphological structures. 15 in Larval Psephenidae (Coleoptera: Byrrhoidea) of Thailand:Annotated List and Illustrated Key to Genera
Figs. 15–20. Morphological structures. 15) Sinopsephenoides: Stellate tubercles on venter; 16) Sinopsephenoides: Short and moderately narrow cephalic plate; 17) Granuleubria: Ninth abdominal segment entire posteriorly (from Lee et al. 2007); 18) Macroeubria: Ninth abdominal segment emarginated posteriorly; 19) Microeubria: Meso- and metathoracic paratergites truncate laterally; 20) Schinostethus: Meso- and metathoracic paratergites acicular laterally.
Annotation and analysis of the secondary structure elements in the Cytochrome P450 protein family
<p>We collected all currently available structures for proteins in the Cytochrome P450 family and annotated their secondary structure elements using SecStrAnnotator software (https://webchem.ncbr.muni.cz/Wiki/SecStrAnnotator). We used 2nnjA as the template domain for the annotation. Based on these annotations, we analysed the occurrence, length distribution, amino acid sequence, and presence of structural irregularities (β-bulges, 3<sub>10</sub>-helices, π-helices) of each secondary structure element class. We also statistically compared the bacterial vs eukaryotic structures. For the secondary structure element classes with sufficient sequence conservation, the most conserved residue is annotated as the reference residue.</p> <p>Main files:</p> <ul> <li><strong>set_ALL.json</strong> - Set-ALL: list of 1012 protein domains belonging to the Cytochrome P450 family (CATH accession 1.10.630.10 + Pfam accession PF00067, accessed on 7 July 2020, one domain per PDB entry)</li> <li><strong>set_NR.json</strong> - Set-NR: non-redundant list of 183 domains (one domain per UniProt ID)</li> <li><strong>domain_lists_table.tsv</strong> - Overview of Set-ALL and Set-NR and separation into subsets Set-NR-Bact (bacterial), Set-NR-Euka (eukaryotic), Set-NR-Arch (archaeal), Set-NR-Viru (viral)</li> <li><strong>structures/template_2NNJ-template.sses.json</strong> - Manually prepared annotation template (domain 2nnjA)</li> <li><strong>structures/template_2NNJ.cif</strong> - Structure of the template domain (2nnjA)</li> <li><strong>annotations_with_reference_residues_ALL.json, annotations_with_reference_residues_ALL.tsv</strong> - Annotation of secondary structure elements for Set-ALL</li> <li><strong>annotations_with_reference_residues_NR.json, annotations_with_reference_residues_NR.tsv</strong> - Annotation of secondary structure elements for Set-NR</li> <li><strong>aligments_NR</strong> - Multiple sequence alignments for each SSE class (Set-NR)</li> <li><strong>logos_NR</strong> - Sequence logos for each SSE class (Set-NR)</li> <li><strong>plots</strong> - Plots of SSE occurrence, length distribution, contained helix types and beta-bulge occurrence (Set-NR), some plots show the comparison between Set-NR-Bact and Set-NR-Euka</li> <li><strong>statistical_tests.ods</strong> - Comparison of SSE occurrence between Set-NR-Bact and Set-NR-Euka by the test of equal proportions and the Fisher test, comparision of the SSE length by the Kolmogorov-Smirnov test and the two-sample Wilcoxon test</li> </ul>
Data from: Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models
The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative. Our results show that the subset of genes chosen for manual annotation by a research community (3.5-7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species' gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities. In our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative.
FIGURE 2 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 2. Habitat types found at the Laje de Santos Marine State Park.
The raw data needed for benchmarking the use of Foldseek for structure-based domain annotation
<p>For more information refer to:<br>https://github.com/Pooryamb/BenchmarkingFS </p>
Data from: Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models
Open the record for dataset details and reuse information.
Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer
GEO Series GSE24704. Caenorhabditis elegans. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The identification and functional annotation of RNA structures conserved in vertebrates
GEO Series GSE87214. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
DomainMapper: Accurate Domain Structure Annotation Including Those with Non-contiguous Topologies
<p>Mapped domains of all proteomes performed in the study "DomainMapper: Accurate Domain Structure Annotation Including Those with Non-contiguous Topologies"</p> <p>All files were created with DomainMapper 3.0.1</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.