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61 results for “sequence similarity”
Figure 1 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Figure 1 - Diversity indexes and accumulation curves for a Illumina and b cultivation data of fungal leaf-inhabiting endophytes of beech. Except of the accumulation curves of cultivation data, both methods revealed a clear and partly significant trend of higher fungal diversity at the valley site.
Fig. 1 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes
Fig. 1 Location of the sampled lakes in the French Northern Alps
Data from: Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms
BACKGROUND: A detailed knowledge about spatial and temporal gene expression is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now simultaneously identify the transcribed part of a species genome and estimate levels of gene expression. RESULTS: mRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads, together with publicly available expressed sequence tag (EST) data from Norway spruce, was used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 83.5% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression differences between samples collected under dark and light conditions. CONCLUSIONS: Our study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6 x 10-09 and 1.1 x 10-09) is an order of magnitude smaller than values reported for angiosperm herbs. However, if one takes generation time into account, most of this difference disappears. The estimates of the dN/dS ratio (non-synonymous over synonymous divergence) reported here are in general much lower than 1 and only a few genes showed a ratio larger than 1.
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
Metadata supporting the AFDB90v4 annotated sequence similarity network
<p>Driven by the development and upscaling of fast genome sequencing and assembly pipelines, the number of protein-coding sequences deposited in public protein sequence databases is increasing exponentially. Recently, the dramatic success of deep learning-based approaches applied to protein structure prediction has done the same for protein structures. We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database. These models cover most of the catalogued natural proteins, including those difficult to annotate for function or putative biological role based on standard, homology-based approaches. In this work, we quantified how much of such "dark matter" of the natural protein universe was structurally illuminated by AlphaFold2 at a high predicted accuracy and modelled this diversity as an interactive sequence similarity network that can be navigated at <a href="https://uniprot3d.org/atlas/AFDB90v4">https://uniprot3d.org/atlas/AFDB90v4</a>. The dataset deposited here corresponds to the metadata generated, and that makes the base of the similarity network constructed and its interpretation. These files are either generated or processed using the code available at <a href="https://github.com/ProteinUniverseAtlas/AFDB90v4">https://github.com/ProteinUniverseAtlas/AFDB90v4</a>.</p> <p>This repository further contains the detailed, individual sequence similarity networks (in CLANS format) generated for the 3 example protein (super)families described in the text.</p> <p>The full content of this repository includes:</p> <ol> <li> <p><strong>AFDBv4_pLDDT_diggestion_UniRef50_2023-02-01.csv</strong>: table listing all uniref50 clusters in UniProt, including information on structural representatives from AFDB. Each column provides different annotations, including functional brightness, median and best pLDDT, brightness and structural representatives, etc.</p> </li> <li> <p><strong>AFDBv4_DUF_dark_diggestion_UniRef50_2023-02-06.csv</strong>: table listing all uniref50 clusters in UniProt and whether they include proteins mapped to known domains of unknown function (DUF).</p> </li> <li> <p><strong>AFDBv4_90.fasta</strong>: fasta file with the sequences of all UniRef50 clusters selected, and used for the all-against-all mmseqs searches that make the base of the network.</p> </li> <li> <p><strong>AFDB90v4_data.csv</strong>: the subset of file (1) that corresponds to the AFDB90v4 dataset, including columns such as functional brightness, median and best pLDDT, brightness and structural representatives, etc.</p> </li> <li> <p><strong>AFDB90v4_data_with_graph_labels.csv</strong>: table listing each individual uniref50 cluster included in the AFDB90v4 dataset, together with their mapping to communities, and connected components.</p> </li> <li> <p><strong>AFDB90v4_cc_data.csv</strong>: table of uniref50 clusters in connected components, including their annotations, and the columns in file (5).</p> </li> <li> <p><strong>AFDB90v4_cc_data_uniprot_community_taxonomy_map.csv</strong>: mapping of each uniprotAC entry to their corresponding component, community and taxonomy.</p> </li> <li> <p><strong>AFDB90v4_subgraphs_summary.csv</strong>: table summarising the properties of individual connected components, including the average brightness, the number of members, the number of unique protein sequences, the median length, and the number of communities.</p> </li> <li> <p><strong>communities_summary.csv</strong>: table summarising the properties of individual communities, including average brightness, the number of members, the number of unique protein sequences, the median length, the most common superkingdom represented, the average structure outlier score, etc.</p> </li> <li> <p><strong>communities_edge_list-coordinates.csv</strong>: the coordinates of each community in the graphical representation. Singleton communities or singleton UniRef50 clusters are not included.</p> </li> <li> <p><strong>communities_edge_list_no_duplicates.csv</strong>: list of edges making the graph.</p> </li> <li> <p><strong>node_class.json</strong>: map between each Uniref50 cluster and its corresponding component and community.</p> </li> <li> <p><strong>subgraphs.tar.gz</strong>: tar file containing gml files for each individual connected component.</p> </li> <li> <p><strong>AFDB90v4_outlier_scores.tsv</strong>: table containing the outlier scores for each community representative.</p> </li> <li> <p><strong>AFDB90v4_dark_galaxies_summary.csv</strong>: table containing the summary of all dark connected components, including average brightness, median length, representatives, number of communities, etc.</p> </li> <li> <p><strong>AFDB90v4_uniprot_naming_assessment_counts.csv</strong>: table listing the per-component semantic diversity scores, as well as the major source of the titles of the proteins included and their count.</p> </li> <li> <p><strong>uniprot_naming_assessment.tar.gz</strong>: tar file containing the per community assessment of predicted protein names in UniProt as of February 2023.</p> </li> <li> <p><strong>CLANS_files.tar.gz</strong>: stores the 3 sequence similarity networks, in CLANS format, constructed for the analysis of the sequence diversity and sequence similarities of the proteins in components, 27, 159 and 3314. These CLANS files make the base of panel A in all figures 3 and 4 and extended data figure 5.</p> </li> </ol> <p> </p>
Data from: Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms
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Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
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Australian long-finned pilot whales (Globicephala melas) emit stereotypical, variable, biphonic, multi-component, and sequenced vocalisations, similar to those recorded in the northern hemisphere
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Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (protein binding microarray data set)
GEO Series GSE110653. Drosophila melanogaster. 2 samples. Type: Genome binding/occupancy profiling by array.
miRNA expression in family with sequence similarity 222 member B (Fam222B) knockdown B16 cells
GEO Series GSE289508. Mus musculus. 2 samples. Type: Non-coding RNA profiling by array.
Single cell RNA and TCR sequencing reveals substantive similarities between synovial fluid and synovial tissue T-cells in inflammatory arthritis.
GEO Series GSE250242. Homo sapiens. 21 samples. Type: Expression profiling by high throughput sequencing.
The bZIP mutant CEBPB(V285A) has sequence specific DNA binding propensities similar to CREB1
GEO Series GSE112020. synthetic construct; Mus musculus. 31 samples. Type: Other.
Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors
GEO Series GSE110654. Drosophila melanogaster. 39 samples. Type: Genome binding/occupancy profiling by array; Genome binding/occupancy profiling by high throughput sequencing.
The bZIP mutant CEBPB(V285A) has sequence specific DNA binding propensities similar to CREB1 [CEBPMut_5mCG]
GEO Series GSE112019. synthetic construct; Mus musculus. 10 samples. Type: Other.
Illumina SBS sequencing and DNBSEQ perform similarly for single-cell transcriptomics
GEO Series GSE277740. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Similarity Regression predicts evolution of transcription factor sequence specificity
GEO Series GSE121420. synthetic construct. 682 samples. Type: Other.
Variations in the expression pattern and sequence similarity of the key genes involved in the metabolism of taxoids among three Taxus species
GEO Series GSE121523. Taxus x media; Taxus mairei; Taxus cuspidata. 9 samples. Type: Expression profiling by high throughput sequencing.
Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (ChIP-seq data set)
GEO Series GSE107059. Drosophila melanogaster. 37 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
FIGURE. Phylogram of Tolypocladium generated from Maximum likelihood analysis of ITS, SSU and LSU sequence data. Purpureocillium lilacinum (CBS 284.36) was selected as an outgroup taxon. The tree topology of the ML analysis was similar to the BI. Maximum likelihood bootstrap values greater than 75 and Bayesian posterior probabilities over 0.90 were indicated above the nodes. The scale bar indicates 0.006 changes. The new species was in blue. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. Phylogram of Tolypocladium generated from Maximum likelihood analysis of ITS, SSU and LSU sequence data. Purpureocillium lilacinum (CBS 284.36) was selected as an outgroup taxon. The tree topology of the ML analysis was similar to the BI. Maximum likelihood bootstrap values greater than 75 and Bayesian posterior probabilities over 0.90 were indicated above the nodes. The scale bar indicates 0.006 changes. The new species was in blue.
aCGH Detects Copy Number Variation with Similar Resolution to PacBio Sequencing Approaches
GEO Series GSE141976. Haplochromis burtoni; Neolamprologus brichardi; Pundamilia nyererei; Oreochromis niloticus; Maylandia zebra. 4 samples. Type: Genome variation profiling by genome tiling array.
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DANDI Archive for NWB datasets
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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.