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Figure 4 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 4. Maximum likelihood-based phylogeny, with 100 bootstrap replicates and using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, with sequences derived from GenBank. GenBank accession numbers are given in parentheses. Colours represent Tropostreptus sample origins. The upper right inset shows the topology of the Tropostreptus hamatus lineage, enlarged to clarify the branching order. Only support values <100 are shown. *Thyropygus sp. (red font) is very likely to be a species misidentification; for more information, see Discussion text.
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, derived from GenBank. GenBank accession numbers are provided in parentheses. Blue bars indicate the 95% highest probability density intervals for node ages. Age estimation for lineage divergence was based on a general arthropod mitochondrial DNA substitution rate and should be considered with caution. *Thyropygus sp. (red font) is very likely to be a misidentification; for more information, see the Discussion.
Figure 1 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 1. Typical Tropostreptus appearance exemplified by a Tropostreptus hamatus individual from Udzungwa Mountains, Tanzania (photograph credit: Nikolaj Scharff).
Figure 2 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 2. Map showing the origin of the millipede specimens used in the study, with the accuracy of location restricted to mountain blocks. Coloured circles all represent Tropostreptus species, whereas grey symbols represent species from other millipede genera. Base map published by permission of the Eastern Arc Mountains Conservation Endowment Fund.
Figure 3 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 3. The gene order of mitochondrial coding sequences shared among all analysed millipede species in this study, which include all known species of Tropostreptus (T. droides, T. hamatus, T. kipunji, T. microcephalus, T. severus and T. sigmatospinus), in addition to Archispirostreptus gigas, Chaleponcus netus, Macrolenostreptus orestes, Prionopetalum kraepelini and Pseudotibiozus cerasopus. Colour key: red, ribosomal RNA (rRNA); pink, transfer RNA (tRNA); yellow, protein-coding sequences (CDS). Arrows indicate gene transcription orientation.
dudesdb_201709 - Fungi and Virus - RefSeq - Complete Genomes
<p>bowtie2 index and dudes database for the set of Fungal and Viral complete genomes from NCBI RefSeq, dating from 2017-09. The dudes database was made based on accession version numbers (DUDesDB.py option -m "av").</p>
dudesdb_201709 - Archaea and Bacteria - RefSeq - Complete Genomes
<p>bowtie2 index and dudes database for the set of Archaeal and Bacterial complete genomes from NCBI RefSeq, dating from 2017-09. The dudes database was made based on accession version numbers (DUDesDB.py option -m "av").</p>
dudesdb_201503 - Archaea and Bacteria - RefSeq - Complete Genomes
<p>bowtie2 index and dudes database (.ddb for version 0.06 and .npz for version 0.07) for the set of Archaeal and Bacterial complete genomes from NCBI RefSeq, dating from 2015-03. The dudes database was made based on accession version numbers (DUDesDB.py option -m "av").</p>
FIGURE 2 in Complete mitochondrial genome of four Scleromystax barbatus (Siluriformes: Callichthyidae) populations
FIGURE 2 | Phylogenetic analysis of 13 Corydoradinae and Hoplosternum littorale (Callichthyinae member) species as the outgroup based on the nucleotide sequences of 13 PCGs from the mitochondrial genome. Bootstrap values are shown next to nodes and the scale bar shows 0.03 changes. Population codes in Tab. 1.
FIGURE 1 in Complete mitochondrial genome of four Scleromystax barbatus (Siluriformes: Callichthyidae) populations
FIGURE 1 | A. Geographic location of the Scleromystax barbatus populations in coastal Atlantic Rainforest rivers. B. Male of S. barbatus. Photo by Caio Feltrin. C. Complete mitochondrial genome of S. barbatus from the AR population. Population codes in Tab. 1.
Figure 5 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 5. Comparison of the nucleotide sequences of the two putative control regions in the mitogenome of P. eriobotryae. The structural elements were recognized: repeat unit, TATA motif, TA(A)n motif, stem and loop, Poly T-stretch sequence, A + T-rich sequence and G(A)nT motif.
Figure 6 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 6. Gene rearrangement, transposition, inversion and inverse transposition. A. Comparison with the ancestor gene sequence of arthropods, Drosophila yakuba and P. eriobotryae gene sequence. B. Comparison with P. eriobotryae and other five known mitogenomes of Phlaeothripidae species. Yellow blocks show PCGs, blue ones show tRNA, red ones show rRNA and Colourless ones show CRs. Red dashes boxes represent conserve gene blocks. Red dotted ovals represent that the reverse transposition happened in the gene blocks. '+' indicates H-strand, and '-' indicates L-strand. Black arrows indicate the direction of gene translation.
Figure 1 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 1. The circular representation of the complete mitogenome of P. eriobotryae. The direction of gene transcription is indicated by the arrows. PCGs are showed as blue purple arrows, rRNA genes as green arrows, tRNA genes as pink purple arrow and CRs as orange arrows. The inner black circles show GC content and GC-skew plotted as the deviation from the average value of the entire sequence. The image was taken from slide-mounted specimen with an Olympus BX53 and edited manually in Adobe Photoshop 2022 v23.0.2.101.
Figure 4 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 4. Putative cloverleaf secondary structures of the 22 tRNAs of P. eriobotryae. The dot "." indicated mismatched base pairs.
Figure 3 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 3. The ratios of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks), and the ratio of Ka/Ks for each PCGs in the mitogenome of P. eriobotryae.
Figure 7 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 7. Phylogenetic tree of thrips obtained from Maximum-likelihood and MrBayes based on 13 PCGs dataset. The numbers on branches are superimposed with bootstrap support values (BP) and the Bayesian posterior probability (PP).
Figure 2 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 2. Codons distribution and usage in the mitogenome of P. eriobotryae. A. Amino acid composition: codon families are provided on the x-axis; numbers of codons of each amino acid are provided on the y-axis. B. The relative synonymous codon usage (RSCU).
Figure 3 in The complete mitochondrial genome of Barbatula quignardi (Băcescu-Meşter, 1967) (Teleostei, Nemacheilidae)
Figure 3. – Maximum Likelihood phylogenetic tree of Barbatula mitogenomes; bootstrap values beside the nodes.
Figure 1 in The complete mitochondrial genome of Barbatula quignardi (Băcescu-Meşter, 1967) (Teleostei, Nemacheilidae)
Figure 1. – Voucher of the sequenced mitogenome, MNHN- IC-2010-1064 (FFFtag4260), 41.7 mm SL, Lez River at Prades-leLez (Hérault Dept.), 24th Nov. 2010, Denys and ONEMA coll.
Figure 2. – Maximum Likelihood phylogenetic tree inferred with the 13 in The complete mitochondrial genome of Thymallus thymallus (Linnaeus, 1758) (Actinopterygii, Salmonidae) obtained by long range PCRs and double multiplexing
Figure 2. – Maximum Likelihood phylogenetic tree inferred with the 13 protein coding genes. The values of bootstrap are represent- ed beside the nodes.
ScienceDex guides
Understand access before you commit
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.