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120 results for “barcode sequence”
Fig. 3 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 3. Phylogenetic position of Macrobiotus sp., Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
Fig. 1 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 1. Phylogenetic position of D. lindholmi and L. a. exigua, Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns (repository for Genome Research paper, 2022)
<p>Simulated ONT and PacBio RNA-Seq data for "Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns" paper (Mikheenko et al., Genome Research, 2022). All details can be found in the Methods section of the paper.</p> <p><strong>PacBio.simulated_uniform_coverage.fasta.gz</strong> and <strong>ONT.simulated_uniform_coverage.fasta.gz files</strong> were used in Supplemental Note “Benchmarking of the read-to-isoform assignment algorithm”.</p> <p><strong>ONT.simulated_real_expression.fasta.gz</strong> file and all GTF files were used in the Section "Splice site correction improves transcript discovery precision". <strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong> was used as the annotation file for all tools. <strong>mouse.gencode.M26.spatial.15percent.expressed.gtf </strong>contains the set of all expressed isoforms. <strong>mouse.gencode.M26.spatial.15percent.expressed_kept.gtf</strong> contains those of the isoforms that are in presented in the annotation file ("known" transcripts), <strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong> contains expressed isoforms that were removed from the annotation ("novel" transcripts).</p>
Data and processing scripts for PRISM barcode sequencing data used in "Massively parallel pooled screening reveals genomic determinants of nanoparticle-cell interactions"
<p>Sequencing data for the PRISM barcodes generated after nano-particle treatment is presented in this repository alongside the code to process the sequencing counts to generate the binning probabilities and weighted scores. <br> <br> For the details please see the original publication or the bioarxiv preprint: https://doi.org/10.1101/2021.04.05.438521<br> <br> The raw data is provided in PILOT_DATA_COUNTS.csv and EXPERIMENT_DATA_COUNTS.csv files, for the pilot and the actual experiment. <br> <br> For each of these files an R script is provided to process them, along with the output of the scripts (PILOT_DATA_PROBABILITIES.csv and EXPERIMENT_DATA_PROBABILITIES.csv)</p>
COI Barcode sequences for arthropod species from the high Appalachian Mountains, USA
<p>Developing systematic conservation plans depends on a wealth of information on a region's biodiversity. For 'dark taxa' such as arthropods, such data is usually very incomplete and in most cases left out from assessments.</p> <p>Sky islands are important and often fragile biodiversity hotspots. Southern Appalachian high-elevation spruce-fir forests represent a particularly threatened sky-island ecosystem, hosting numerous endemic and threatened species, but their arthropods remain understudied.</p> <p>Here we use voucher-based megabarcoding to explore genetic differentiation among leaf-litter arthropod communities of these highlands, and to examine the extent to which they represent dispersed communities of more or less coherent species, manageable as a distributed unit. We assembled a dataset comprising >6000 COI sequences representing diverse arthropod groups to assess species richness and sharing across peaks and ranges. Comparisons were standardized across taxa using automated species delimitation, measuring endemism levels by putative species.</p> <p>Species-richness was high, with sites hosting from 86-199 litter arthropod species (not including mites or myriapods). Community profiles suggest that around one-fourth of these species are unique to single sky islands and more than one-third of all species are limited to a particular range. Across major taxa, endemicity was lowest in Araneae, and highest in neglected groups like Isopoda, Pseudoscorpionida, Protura, and Diplura.</p> <p>Southern Appalachian sky islands of spruce-fir habitat host significantly distinct leaf litter arthropod communities, with high levels of local endemicity. This is the first work to provide such a clear picture of peak and range uniqueness for a taxonomically broad sample. Ensuring the protection of a sizeable fraction of high-elevation litter species richness will therefore require attention at a relatively fine spatial scale.</p>
Expanded phylogeny of Nomadinae (Hymenoptera: Apidae) with integration of UCE and DNA barcode sequence data
Open the record for dataset details and reuse information.
Dual randomly barcoded transposon sequencing (Dual Tn-seq) data for <em>Streptococcus pneumoniae</em> D39
Open the record for dataset details and reuse information.
COI Barcode sequences for arthropod species from the high Appalachian Mountains, USA
Open the record for dataset details and reuse information.
Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding
<p>Description of 1200bp amplicon primer sets and .bed and .tsv files for SARS-CoV-2 assembly using the ARTIC bioinformatics pipeline.</p>
Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma.
<p>Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma</p>
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a in A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadinae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a number of named, primarily Palaearctic taxa included. Species groups that are characterizable morphologically and discussed are indicated in different colours. The tree is rooted using Heterogamus species.
FIGURE 1 in Additional description on morphology of the Misol snake eel from Taiwan, with four verified barcodes of life sequences
FIGURE 1. Lateral view of Yirrkala misolensis. (A) Before fixing, TOU-AE7866, 351 mm TL with broken tail, Ke-tzu-liao fish market, Kaohsiung, Taiwan. Scale represents 10 mm. The position of dorsal fin origin and vent marked with red arrows. The center is a close-up view of cephalic part (Photo by W. -C. Huang). (B) When preserved, NMMB-P12003, 486 mm TL, mature female, Dong-gang fish market, Ping-tung, Taiwan, the position of dorsal fin origin and vent marked with pins.
FIGURE 3 in Additional description on morphology of the Misol snake eel from Taiwan, with four verified barcodes of life sequences
FIGURE 3. Neighbor-joining tree based on CO1 sequences, constructed using the specimens mentioned in the present study and 1 congener from NCBI. The bar indicates the evolutionary distances which were computed using the Kimura 2-parameter method with 10,000 bootstrap-replicated.
FIGURE 2 in Additional description on morphology of the Misol snake eel from Taiwan, with four verified barcodes of life sequences
FIGURE 2. Illustration of Yirrklala misolensis, NMMB-P12003, 486 mm TL, mature female, Dong-gang fish market, Pingtung, Taiwan. (A) Lateral view of head, arrows show the position of frontal pore and supratemporal pore. (B) Dentition.
Supplementary material 1 from: Binh HT, Ngoc NV, Tagane S, Toyama H, Mase K, Mitsuyuki C, Strijk JS, Suyama Y, Yahara T (2018) A taxonomic study of Quercus langbianensis complex based on morphology, and DNA barcodes of classic and next generation sequences. PhytoKeys 95: 37-70. https://doi.org/10.3897/phytokeys.95.21126
Figure S1, S2 : Explanation note: Figure S1. Bayesian phylogeny of 29 samples of Quercus and one Trigonobalanus (outgroup) based on ITS sequences. Branches are labeled with posterior probabilites. Figure S2. Bayesian phylogeny of 29 samples of Quercus and one Trigonobalanus (outgroup) based on concatenated rbcL and matK sequences. Branches are labeled with posterior probabilities.
FIGURE 20 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 20. Phylogram of a maximum likelihood analysis of the DNA sequence data (Appendix 4) using the general time reversible model. The analysis includes the subaptera – group taxa and one outgroup.
FIGURE 19 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 19. Strict consensus tree (length 374 steps, CI 0.94, RI 0.90) of a maximum parsimony analysis of the DNA sequence data (Appendix 4). Maximum parsimony bootstrap values> 50 % are shown above branches (2000 replications). The analysis includes the subaptera – group taxa and one outgroup.
FIGURE 17 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 17. Distribution of the bisexual species of the subaptera-group: Phyllodromica iberica morph #1, #2 and #3, and P. quadracantha; these species only occur on the Iberian Peninsula. In cases where two different symbols partly overlap, two P. iberica morphs are found at the same locality; in one case all three morphs occur together (Fig. 15, Sp 510 ca. 1° W, 40° N). P. iberica morph #3 symbols labeled with a "+" (Fig. 15, Sp 335) or an " " (Fig. 15, Sp 186, 270, 469 and 512) indicate the presence of morphological variations. At some localities no males have been found ("sad face" symbol) but females with spermathecae containing sperms and/or with oothecae containing male and female offspring. Both facts indicate the presence of a bisexual species of unknown specifity.
FIGURE 16 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 16. Distribution of bisexual species of the subaptera-group and the parthenogenetic species P. subaptera on the Iberian peninsula.
FIGURE 14 Phyllodromica quadracantha, male. A in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 14 Phyllodromica quadracantha, male. A membrane glands of the right lateral region of the anterior border of tergite 6. B right paraproct with bulge on the medio-anterior process (compare Fig. 5 D). C distal end of tibia from the right mid leg (bearing 4 distal tibia spines; compare Fig. 5 E) in posterior view. D helmet sclerite, the nomenclature "fr" and "re" do not indicate the orientation of the sclerite within the animal. E–G tergites 6 (E), 7 (F) and 8 (G) of specimen with slightly different tergal structures on tergite 7. Due to unnatural squeezing of the tergite 8 (G) during the mounting procedure the distance between the anterior processes appears broader than under natural conditions. Abbreviations: fr "frontal" part of helmet sclerite, bf bristle field, bu bulge, hs helmet sclerite, mg membrane glands, mp medio-anterior process of right paraproct, re "rear" of helmet sclerite, r ridge, rp right paraproct, sp spinelike process, tar tarsus, tib tibia, tr transversal trough. Same scale for (A–D) and (F–G). Identification: (A, E–G) Sp 504a/M1, (B, C) Sp 203d/ M1(holotype). (D) Sp 203b/M7.
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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.