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19,342 results for “Sequence”
FIG. 2 in A journey through Cyanobacteria in Brazil: a review of novel genera and 16S rRNA sequences
FIG. 2. — Flowchart of search methods for identification and selection of Brazilian 16S rDNA sequences from GenBank (NCBI).
Enhanced Sequence-Activity Mapping and Evolution of Artificial Metalloenzymes by Active Learning
<p>This entry contains data, pretrained models and supplementary files for our enzyme engineering study:</p> <p><strong>Title:</strong> Enhanced Sequence-Activity Mapping and Evolution of Artificial Metalloenzymes by Active Learning<br><strong>Journal:</strong> ACS Central Science</p> <p>If you use any of the data or code in the <a href="https://github.com/lasgroup/ml-protein-design-sav-gold">repository</a>, please cite the paper.</p> <p>The contents of this entry are:</p> <ol> <li>Sequence embeddings needed for reproducing the code are found in data.zip. Unzip the contents of the folder to <code>/data</code> in the code structure. </li> <li>NGS sequencing analysis and raw data in <code>NGS analysis.zip</code></li> <li>10% subset of structures generated with the Rosetta software in <code>structures.zip</code></li> <li>Pretrained and saved models for plotting, clustering and further prediction are saved in <code>models.zip</code></li> <li>Raw assay data including our designed libraries by active learning are found in <code>assay_and_ML_data.zip</code></li> </ol>
Human intestinal Bacteria Collection (HiBC): Genome sequences
<p>The <a href="https://hibc.rwth-aachen.de/" target="_blank" rel="noopener">Human intestinal Bacteria Collection (HiBC)</a> is a collection of bacterial strains, isolated from the human gut for which 16S rRNA gene sequences, genome sequences and culture conditions are made available to the research community. In addition to previously described bacteria, we include strains that represent novel species which have been taxonomically described and validly named, or will be in the future. This collection will be updated regularly.</p> <p>This dataset includes the genome sequences of the isolates in the FASTA nucleotide format. Plasmids sequences when present are located at the very end of the file.</p> <p><strong>UPDATE v3</strong>: The genome of one of our isolate had been unfortunately swapped. This mistake has been now corrected on Zenodo and Coscine. The genome of <em>Segatella sinensis</em> CLA-AA-H117 should be considered correct with 103 contigs and 3 671 232 nt. Please note that the genome available at the NCBI is the correct one (GCA_040324585.2). Two typos regarding taxonomy have been corrected as well: <em>Maccoya intestinihominis</em> has been corrected to <em>Maccoyia intestinihominis</em> and <em>Faecousia faecis</em> to <em>Faecousia intestinalis</em>.</p>
Fig. 3 in Molecular phylogeny of Indonesian Lymantria Tussock Moths (Lepidoptera: Erebidae) based on CO I gene sequences
Fig. 3. Neighbor-Joining tree based on K2P distance model of all substitutions of CO I gene (Bootstrap support are shown at the nodes; ID=specimens from Indonesia).
Fig. 1 in First complete mitogenome sequence of Korean Gloydius ussuriensis (Viperidae: Crotalinae)
Fig. 1. Maximum likelihood (ML) phylogenetic tree constructed with 37 viper mitogenomes, based on 13 concatenated protein-coding genes. Achalinus meiguensis (FJ424614) was used as an outgroup species and bootstrap values are shown at the nodes. The mitogenome of Gloydius ussuriensis (OR680782) was determined in this study.
Fig. 4. Maximum likelihood tree for 43 in Molecular phylogeny of Indonesian Lymantria Tussock Moths (Lepidoptera: Erebidae) based on CO I gene sequences
Fig. 4. Maximum likelihood tree for 43 species of Lymantria based all substitutions of CO I gene (Bootstrap support are shown at the nodes; ID=specimens from Indonesia).
Figure 12 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 12. Columnar section of the Cenomanian–Turonian boundary and the Lower and Middle Turonian part of the Wunstorf core Wu 2010/4 with agglutinated foraminiferal morphogroups, Fisher alpha index, species richness, and foraminiferal events (acmes) indicated by arrows. For log legend, see Fig. 4.
Figure 11 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 11. Columnar section of the Cenomanian part of the Baddeckenstedt quarry with agglutinated foraminiferal morphogroups, Fisher alpha index, species richness, and foraminiferal events (acmes) indicated by arrows. For log legend, see Fig. 3; log redrawn after Wilmsen (2003: Fig. 8).
Figure 6 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 6. Late Albian to Turonian agglutinated foraminifera from the Lower Saxonian Cretaceous; scale bars are 100 µm. (a) Saccammina grzybowski, Wunstorf Wu2010/1, 54.00 m. (b) Psammosphaera fusca, Wunstorf Wu2010/1, 59.05 m. (c) Tipeammina elliptica, Söhlde section, 31.00 m. (d–e) Tipeammina sp. 1, Wunstorf Wu2010/4, 43.30 m. (f) Hyperammina gaultina, Wunstorf Wu 2010/4, 48.20 m. (g–h) Ammolagena clavata, two specimens sticking together, Wunstorf Wu2010/3, 25.50 m. (i) Ammolagena contorta, possibly previously attached on an inoceramid prism, Wunstorf Wu2010/4, 38.20 m. (j) Caudammina ovula, Söhlde section, 31.00 m. (k) Subreophax scalaris, Wunstorf Wu2010/1, 69.10 m. (l) Ammodiscus cretaceus, Wunstorf Wu 2010/4, 48.20 m. (m) Ammodiscus glabratus, Wunstorf Wu2010/1, 54.65 m. (n) Ammodiscus peruvianus, Wunstorf Wu2010/1, 54.00 m. (o) Ammodiscus tenuissimus, Wunstorf Wu2010/4, 43.30 m. (p) Glomospira diffundens, Wunstorf Wu2010/1, 49.05 m. (q) Glomospira gordialis, Wunstorf Wu 2010/3, 66.05 m. (r) Repmanina charoides, Wunstorf Wu2010/4, 38.20 m. (s) Lituotuba lituiformis, Wunstorf Wu 2010/4, 48.95 m. (t) Rzehakina minima, Wunstorf Wu2010/1, 54.80 m.
Figure 8 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 8. Late Albian to Turonian agglutinated foraminifers from the Lower Saxonian Cretaceous; scale bars are 100 µm. (a) Tritaxia gaultina, Wunstorf Wu2010/1, 19.05 m. (b) Tritaxia tricarinata, Wunstorf Wu2010/1, 19.05 m. (c) Tritaxia macfadyeni, Wunstorf Wu2010/1, 34.10 m. (d–e) Eggerellina brevis, Baddeckenstedt section, 19.30 m. (f) Eggerellina mariae, Wunstorf Wu2010/3, 30.15 m. (g) Flourensina intermedia, Wunstorf Wu2010/1, 54.80 m. (h) Gaudryina sp. 1, Baddeckenstedt section, 39.00 m. (i) Verneuilinoides sp., Wunstorf Wu2010/4, 48.95 m. (j) Vialovella frankei, Wunstorf Wu2010/1, 15.20 m. (k) Arenobulimina bochumensis, Baddeckenstedt section, 9.00 m. (l) Arenobulimina preslii, Wunstorf Wu2010/4, 43.30 m. (m) Arenobulimina truncata, Wunstorf Wu2010/4, 43.30 m. (n–o) Ataxophragmium depressum, Wunstorf Wu2010/4, 58.60 m. (p) Hagenowella elevata, Wunstorf Wu2010/4, 58.60 m. (q) Voloshinoides advenus, Wunstorf Wu2010/1, 29.25 m. (r) Voloshinoides anglicus, Baddeckenstedt section, 7.00 m. (s) Pseudotextulariella cretosa, Wunstorf Wu2010/1, 19.05 m. (t) Kadriayina gradata, Wunstorf Wu2010/3, 66.05 m. (u) Marssonella ozawai, Wunstorf Wu2010/1, 15.20 m.
Figure 3 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 3. Schematic locality details of the study area of Wunstorf and position of the cores: green (Voigt et al., 2008b), blue (Erbacher et al., 2020), and red (this study). Modified from Seibertz (2013: Fig. 5).
Figure 9 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 9. Columnar section of the Albian to Cenomanian part of the Wunstorf core Wu 2010/1 with agglutinated foraminiferal morphogroups, Fisher alpha index, species richness, and foraminiferal events (acmes) indicated by arrows. For log legend, see Fig. 3.
Figure 1 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 1. Paleogeographical map of Europe and the study area. (A) Paleogeography of Europe during the Cenomanian, modified after Philip and Floquet (2000). (B) Paleogeography of southern Lower Saxony during the early Cenomanian, modified from Wilmsen et al. (2021), base map from Hiss (1995).
Figure 7 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 7. Late Albian to Turonian agglutinated foraminifers from the Lower Saxonian Cretaceous; scale bars are 100 µm. (a) Reophax subfusiformis, Wunstorf Wu2010/1, 54.00 m. (b) Pseudonodosinella nodulosa, Wunstorf Wu2010/4, 48.20 m. (c) Pseudonodosinella parvula, Wunstorf Wu2010/4, 48.20 m. (d) Pseudonodosinella troyeri, Baddeckenstedt section, 39.00 m. (e) Haplophragmoides suborbicularis, Wunstorf Wu2010/3, 70.50 m. (f) Haplophragmoides walteri, Wunstorf Wu2010/4, 48.95 m. (g) Ammobaculites agglutinans, Söhlde section, 31.00 m. (h) Ammobaculites wenonahae, Wunstorf Wu2010/1, 19.05 m. (i) Bulbobaculites problematicus, Wunstorf Wu2010/1, 24.75 m. (j) Spiroplectammina navarroana, Wunstorf Wu2010/4, 48.20 m. (k) Spiroplectinella cretosa, Baddeckenstedt section, 2.00 m. (l) Bicazammina lagenaria, Söhlde section, 24.00 m. (m) Parvigenerina sp. 3, Wunstorf Wu2010/4, 48.95 m. (n) Eobigenerina kuhnti, Söhlde section, 9.50 m. (o) Eobigenerina variabilis, Söhlde section, 1.50 m. (p) Rectogerochammina eugubina, Wunstorf Wu2010/4, 48.95 m. (q) Gerochammina stanislawi, Wunstorf Wu2010/4, 53.15 m. (r) Plectina cenomana, Wunstorf Wu2010/3, 45.00 m. (s) Plectina mariae, Wunstorf Wu2010/3, 84.00 m.
Figure 4 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 4. Correlated columnar sections of the Wunstorf cores Wu 2010/1 and Wu 2010/3 and their carbon isotope patterns. On the right correlation to the carbon isotopes of the Wunstorf Wu2011/8 core of Erbacher et al. (2020: Fig. 3) and to the Anderten-1 core of Bornemann et al. (2017: Fig. 3). Brown bar: correlation of a sequence boundary based on the isotopic pattern; green bar: correlation based on a bio-event; grey bar: correlation based on a lithoevent.
Figure 2 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 2. Chronostratigraphy, selected events, and depositional sequences as well as interpreted sea level curve of the Lower Saxony Cretaceous. Depositional sequences, associated sequence boundaries, and sea level curve are from Janetschke et al. (2015). Age of stage boundaries are from Gradstein et al. (2020).
Figure 13 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 13. Columnar section of the Cenomanian–Turonian boundary and the Lower to Upper Turonian part of the Söhlde–Loges quarry with agglutinated foraminiferal morphogroups, Fisher alpha index, species richness, and foraminiferal events (acmes) indicated by arrows. For log legend, see Fig. 4; log redrawn after Wiese (2009: Fig. 6).
Figure 10 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 10. Columnar section of the Lower Cenomanian part of the Wunstorf core Wu 2010/3 with agglutinated foraminiferal morphogroups, Fisher alpha index, species richness, and foraminiferal events (acmes) indicated by arrows. For log legend, see Fig. 3.
Figure 14 in Albian to Turonian agglutinated foraminiferal assemblages of the Lower Saxony Cretaceous sub-basins - implications for sequence stratigraphy and paleoenvironmental interpretation
Figure 14. Albian, Cenomanian, and Turonian FOs and LOs (first – and last occurrences) of selected agglutinated foraminifers from Lower Saxony (Wunstorf, Baddeckenstedt, Söhlde), the Münsterland (Frieg and Kemper, 1989) and the English Chalk (Hart et al., 1989), and the DWAF (deep-water agglutinated foraminifera) zonation of the western Tethys (Coccioni et al., 1995; Kaminski et al., 2011).
Fig. 5 – The herein sequenced specimen 10301 in A new hypothesis on the evolution of the hybosorid beetle capacity to conglobate their bodies into a tight ball (Coleoptera: Scarabaeoidea)
Fig. 5 – The herein sequenced specimen 10301 of Ivieolus pseudoscutellatus illustrating all 13 unambiguously optimized morphological apomorphic characters in support of the Ivieolini plus Scarabatermitini clade (character/state numbering follows Ballerio & Grebennikov 2016). Three of these characters (in square brackets and marked with a question mark) need critical re-assessment and perhaps rescoring.
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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.