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52 results for “GenBank”
Assembled "juvenile head region" transcriptome from the hagfish Eptatretus burgeri (NCBI GenBank Accession: SRX2541845)
<p>1) The raw reads were dwonloaded from NCBI GenBank (SRA run accession: (SRR5234495) with sratoolkit.</p> <p>2) The assembly was performed with Trinity with the folllowing parameters:</p> <p>Trinity --seqType fq --max_memory 100G --left eb-hf-head-region-SRR5234495/eb-hf-head-region-SRR5234495_1.fastq --right eb-hf-head-region-SRR5234495/eb-hf-head-region-SRR5234495_1.fastq --CPU 10 --output trinity-transcriptome-eb/</p> <p>3) ORFs were predeicted with TransDecoder with the following settings:</p> <p>TransDecoder.LongOrfs -t transcriptome-eb-hf-head-region.fasta</p> <p>TransDecoder.Predict -t transcriptome-eb-hf-head-region.fasta</p> <p> </p>
Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)"
<p><strong>Abstract:</strong></p> <p>Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardised sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus <em>Cirripectes</em>. Recent studies discovered several <em>Cirripectes</em> species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, in order to evaluate the diversity and distribution of <em>Cirripectes</em> species in the Mascarene Archipelago, a little studied region but an important biodiversity hotspot, complete mitochondrial genomes and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analysed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, <em>Cirripectes castaneus, C. randalli, </em>and <em>C. stigmaticus</em>. <em>C. castaneus</em> and <em>C. stigmaticus</em> both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, <em>C. randalli </em>shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of <em>C. castaneus, C. randalli </em>and <em>C. stigmaticus </em>in Rodrigues, and the presence of <em>C. stigmaticus</em> in Reunion. This study contributes to fill the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g. eDNA).</p> <p><strong>Content of this repository:</strong></p> <p>Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic <em>Cirripectes</em> blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)" published in<em> Ecology and Evolution</em> (2023)</p>
Updating splits, lumps, and shuffles: Reconciling GenBank names with standardized avian taxonomies
Open the record for dataset details and reuse information.
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records in A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined.
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
FIGURE 10 in A new species of Polietina (Diptera: Muscidae) from South America, with an updated phylogeny of the genus and a review of species' identity in GenBank
FIGURE 10. Molecular phylogenetic hypothesis using Bayesian posterior probabilities of COI sequences (644 bp, model = GTR+G) for nine Polietina specimens and two outgroup taxa with Bayesian posterior probability values. Names in italic are those currently at GenBank; names in bold italic are species identity of vouchers after detailed morphological revision. GenBank accession numbers are provided in parentheses. *Wrongly assigned vouchers. See text for explanation.
FIGURES 1–2 in A new species of Polietina (Diptera: Muscidae) from South America, with an updated phylogeny of the genus and a review of species' identity in GenBank
FIGURES 1–2. Male habitus of Polietina ponti sp. nov. (holotype). 1: habitus, lateral view; 2: head, anterior view.
FIGURE 9 in A new species of Polietina (Diptera: Muscidae) from South America, with an updated phylogeny of the genus and a review of species' identity in GenBank
FIGURE 9. Most parsimonious phylogenetic hypothesis obtained with equal weights of the 23 morphological characters for 13 species of Polietina and the three outgroup species. Filled circles represent unique transformations, and empty circles represent homoplastic character state transformations under fast optimization.
FIGURES 4–8 in A new species of Polietina (Diptera: Muscidae) from South America, with an updated phylogeny of the genus and a review of species' identity in GenBank
FIGURES 4–8. Male terminalia of Polietina ponti sp. nov. (paratype). 4: cercal plate, dorsal view, marginal spined processes visible; 5: cercal plate, ventral view, marginal spined processes omitted; 6: right surstylus, lateral view; 7: phallus and associated appendages, lateral view; and 8: fifth sternite, dorsal view. (Scale bar: 0.2 mm)
FIGURE 6. Maximum likelihood tree constructed using COI sequences with GenBank accession numbers. Bootstrap support values were calculated with a rapid bootstrapping algorithm for 1000 in Branchinotogluma bipapillata n. sp., a new branchiate scale worm (Annelida: Polynoidae) from two hydrothermal fields on the Southwest Indian Ridge
FIGURE 6. Maximum likelihood tree constructed using COI sequences with GenBank accession numbers. Bootstrap support values were calculated with a rapid bootstrapping algorithm for 1000 replicates in Raxml, and only those higher than 50 were shown.
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis. in Description of the lucky Cophyla (Microhylidae, Cophylinae), a new arboreal frog from Marojejy National Park in north-eastern Madagascar
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis.
Alignment of ITS sequences of Erysiphe specimens from Koelreuteria hosts, with Golovinomyces spp. as outgroup. The scientific names are followed by the respective GenBank accession number.
Open the record for dataset details and reuse information.
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
Genbank dataset for a paper on the Mediterranean biodiversity hotspot
<p>This folder contains the raw Genbank data to execute the code available at this link: <a href="https://github.com/JanPerret/Biodivmex_git">https://github.com/JanPerret/Biodivmex_git</a></p>
GenBank PLN (Plantae, Fungi, Algae) Sequence Index in TSV, CSV, JSONL formats hash://sha256/bc7368469e50020ce8ae27b9d6a9a869e0b9a2a0a9b5480c69ce6751fa4b870e hash://md5/f6f78f64e3b3ff06adc3229badbd578b
<p>GenBank [1] makes sequence records openly available. </p> <p>This publication contains an index of all accession records from the GenBank PLN division release v256 as seen around 27 June 2023 (2023-06-27) by Preston [2]. PLN division is said to include sequence associated with plants, fungi and algae.</p> <p>included files:</p> <p>00_gbpln.json.gz - gzipped archive of simple line-json representation of records in gbpln sequence archives.</p> <p>00_gbpln.sample.json - first 10 lines of line-json representation of records in gbpln sequence archives.</p> <p>00_gbpln.tsv.gz - gzipped archive of tab-separated values (tsv) representation of records in gbpln sequence archives.</p> <p>00_gbpln.sample.tsv - first 10 lines of tab-separated values (tsv) representation of records in gbpln sequence archives.</p> <p>00_gbpln.csv.gz - gzipped archive of comma-separated values (csv) representation of records in gbpln sequence archives.</p> <p>00_gbpln.sample.csv - first 10 lines of comma-separated values (csv) representation of records in gbpln sequence archives.</p> <p>Also include Preston provenance records in files with 64 long character filenames (e.g., hash://sha256/bc7368469e50020ce8ae27b9d6a9a869e0b9a2a0a9b5480c69ce6751fa4b870e).</p> <p>Please do note that, at time of writing (2023-07-05), the actual GenBank Sequence archives are hosted at Arizona State University Biodiversity Knowledge Integration Center via Preston remote https://biokic6.rc.asu.edu/preston/gbpln . And this ASU remote is currently proxied via https://linker.bio. </p> <p>Examples:</p> <p>To stream json structure data directly from zenodo and only include records with "OBI" in it:</p> <pre><code class="language-bash"># Stream records from this publication # and print first record containing "OBI" in gbpln.json.gz # using bash, jq, gunzip, head, and curl curl https://zenodo.org/record/8117720/files/00_gbpln.json.gz\ | gunzip\ | grep -E "[^a-zA-Z]OBI[^a-zA-Z]"\ | head -n1\ | jq . </code></pre> <p>with expected result:</p> <pre><code class="language-json">{ "accession": "JF951063", "http://www.w3.org/2000/01/rdf-schema#seeAlso": "https://ncbi.nlm.nih.gov/nuccore/JF951063", "definition": "Phalaris californica isolate CAL1ITS 5.8S ribosomal RNA gene and internal transcribed spacer 2, partial sequence.", "organism": "Phalaris californica", "specimen_voucher": "D. Keil s.n. (OBI)", "db_xref": "taxon:1108036", "country": "USA", "http://www.w3.org/ns/prov#wasDerivedFrom": "line:gz:hash://sha256/80f3e67d9a954cc8ca7223a10d1951c1ff84ca2844e7840bcb32eeac61181964!/L1400532-L1400572", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "genbank-flatfile" } </code></pre> <p>Similar example, but using csv :</p> <pre><code class="language-bash"># Stream records from this publication # and print first record containing "OBI" in 00_gbpln.csv.gz # using bash, jq, gunzip, head, and curl curl https://zenodo.org/record/8117720/files/00_gbpln.csv.gz\ | gunzip\ | grep -E "[^a-zA-Z]OBI[^a-zA-Z]"\ | head -n1 </code></pre> <p>with expected results:</p> <pre><code>JF951063,https://ncbi.nlm.nih.gov/nuccore/JF951063,"Phalaris californica isolate CAL1ITS 5.8S ribosomal RNA gene and internal transcribed spacer 2, partial sequence.",taxon:1108036,Phalaris californica,USA,null,D. Keil s.n. (OBI),null,line:gz:hash://sha256/80f3e67d9a954cc8ca7223a10d1951c1ff84ca2844e7840bcb32eeac61181964!/L1400532-L1400572 </code></pre> <p>with header, extracted using:</p> <pre><code class="language-bash">curl https://zenodo.org/record/8117720/files/00_gbpln.csv.gz\ | gunzip\ | head -n1</code></pre> <p> </p> <pre><code>accession,rdfs:seeAlso,definition,db_xref,organism,country,host,specimen_voucher,isolation_source,prov:wasDerivedFrom</code></pre> <p>The same results can be obtained using Preston, a biodiversity dataset tracker:</p> <pre><code class="language-bash">preston ls\ --anchor hash://sha256/bc7368469e50020ce8ae27b9d6a9a869e0b9a2a0a9b5480c69ce6751fa4b870e\ --remote https://linker.bio,https://zenodo.org/record/8117720/files/,https://biokic6.rc.asu.edu/preston/gbpln\ | grep urn:x-ncbi:gbpln.csv.gz\ | head -n1\ | preston cat\ --remote https://linker.bio,https://zenodo.org/record/8117720/files/,https://biokic6.rc.asu.edu/preston/gbpln\ | gunzip\ | grep -E "[^a-zA-Z]OBI[^a-zA-Z]"\ | head -n1 </code></pre> <p>References </p> <p>[1] Sayers E, Cavanaugh M, Clark K, Ostell J, Pruitt K, Karsch-Mizrachi I, "GenBank", Nucleic Acids Research, Volume 47, Issue D1, January 2019, pp. D94-D99 PMID:30365038 PMCID:PMC6323954 DOI:10.1093/nar/gky989</p> <p>[2] Elliott, M.J., Poelen, J.H. & Fortes, J.A.B. Signing data citations enables data verification and citation persistence. Sci Data 10, 419 (2023). doi:10.1038/s41597-023-02230-y hash://sha256/f849c870565f608899f183ca261365dce9c9f1c5441b1c779e0db49df9c2a19d</p> <p>PS To clone all data (including >200GB source data):</p> <pre><code class="language-bash">preston clone\ --remote https://linker.bio,https://zenodo.org/record/8117720/files/,https://biokic6.rc.asu.edu/preston/gbpln\ --anchor hash://sha256/bc7368469e50020ce8ae27b9d6a9a869e0b9a2a0a9b5480c69ce6751fa4b870e </code></pre>
NCBI GenBank bacterial sequence assemblies 1/4
<p>Bacterial genomes and scaffolds downloaded from the NCBI GenBank assembly database (part 1/4).</p>
NCBI GenBank bacterial sequence assemblies 2/4
<p>Bacterial genomes and scaffolds downloaded from the NCBI GenBank assembly database (part 2/4).</p>
NCBI GenBank bacterial sequence assemblies 4/4
<p>Bacterial genomes and scaffolds downloaded from the NCBI GenBank assembly database (part 4/4).</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.