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133 results for “gene annotation”
Revised gene annotations for the entemopathogenic nematode, Heterorhabditis bacteriophora.
<p>Revised gene annotations for the entemopathogenic nematode, <em>Heterorhabditis bacteriophora. </em>These annotations were generated using a publicly available <em>Heterorhabditis bacteriophora </em>genome assembly and publicly available RNA-sequencing datasets using BRAKER1. GFF file. </p>
Supplementary Tables on Gene Annotations of 49 Bacillariophyta Genome Assemblies
<p>Supplementary Tables attaining to the manuscript entitled <strong>Annotation of protein-coding genes in 49 diatom genomes from the Bacillariophyta clade. </strong>These Supplementary Tables describe in part the data foundation and results of the actual annotation dataset that is available at <a href="https://doi.org/10.5281/zenodo.13767023" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13767023</a>.</p> <p><strong>Supplementary Table S1</strong>: Genome assemblies available at NCBI Datasets in June 2024.</p> <p><strong>Supplementary Table S2</strong>: Genome assemblies excluded from annotation.</p> <p><strong>Supplementary Table S3</strong>: Accession numbers of genome assemblies and RNAseq libraries used for annotating 49 diatom genomes. Table also lists repeat content of genome assemblies after masking with RepeatModeler2/RepeatMasker.</p> <p><strong>Supplementary Table S4</strong>: Software and container versions used for annotating 49 diatom genomes.</p> <p><strong>Supplementary Table S5</strong>: Summary of EnTAP functional annotation results. The actual functional annotations are included in the annotation dataset that is available at <a href="https://doi.org/10.5281/zenodo.13767023" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13767023</a>.</p>
NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition
<p>The automatic recognition of gene names and their corresponding database identifiers in biomedical text is an important first step for many downstream text-mining applications. The NLM-Gene corpus is a high-quality manually annotated corpus for genes, covering ambiguous gene names, with an average of 29 gene mentions (10 unique identifiers) per article, and a broader representation of different species (including <i>Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Arabidopsis thaliana, Danio rerio,</i> etc.) when compared to previous gene annotation corpora. NLM-Gene consists of 550 PubMed articles from 156 biomedical journals, doubly annotated by six experienced NLM indexers, randomly paired for each article to control for bias. The annotators worked in three annotation rounds until they reached a complete agreement. Using the new resource, we developed a new gene finding algorithm based on deep learning which improved both on precision and recall from existing tools. The NLM-Gene annotated corpus is freely available at Dryad and at <a href="https://www.ncbi.nlm.nih.gov/research/bionlp/">https://www.ncbi.nlm.nih.gov/research/bionlp/</a>. The gene finding results of applying this tool to the entire PubMed/PMC are freely accessible through our web-based tool PubTator.</p>
Gene annotations and associated FASTA file of Antechinus flavipes (yellow-footed antechinus)
<p>Gene annotations of <em>Antechinus flavipes</em> (yellow-footed antechinus) associated with the manuscript "A chromosome-level genome of <em>Antechinus flavipes</em> provides a reference for an Australian marsupial genus with male death after mating" (<em>Molecular Ecology Resources</em>, accepted).</p> <p><strong>Annotation file and associated FASTA files for <em>A. flavipes</em> assembly AdamAnt. </strong><br> • AdamAnt.gff3.tar.gz: EVidenceModeler (EVM) gene model annotation file for <em>A. flavipes</em> assembly AdamAnt.<br> • AdamAnt.CDS.fa.tar.gz: EVM gene models coding sequences.<br> • AdamAnt.AA.fa.tar.gz: EVM gene models coding sequences translated into amino acid sequences.</p> <p><strong>Annotation file and associated FASTA files for <em>A. flavipes</em> transcriptome assembly generated using ROPUS (Reference-guided Ortholog Pipeline for Unannotated species; see doi:10.5281/zenodo.3722900). </strong><br> • antechinus_flavipes_ROPUS_CDS_annotated.fa.tar.gz: ROPUS CDS set. Annotated using human as the reference species.<br> • antechinus_flavipes_ROPUS_AA_annotated.fa.tar.gz: ROPUS AA set. Translated using the CDS sequence. <br> • antechinus_flavipes_ROPUS_annotated.gff3.tar.gz: annotation file for gene expression analysis using the <em>A. flavipes </em>ROPUS CDS FASTA.</p>
Annotation and evolutionary analysis of chemosensory gene sequence data in the Colorado potato beetle, Leptinotarsa decemlineata
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Gene annotations and optical maps of the Aegilops tauschii acc. AL8/78 assembly Aet v6.0
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NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition
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A snakemake toolkit for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims of museum collections
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Data from: Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes
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Taxonomic and functional annotations of the Integrated non-redundant Gene Catalog 9.9
<p>The Integrated non-redundant Gene Catalog (<strong>IGC</strong>) 9.9 is a database of 9.9 million genes from 1267 individual fecal samples together with the Homo sapiens database (MetaHIT project, grant agreement 201052). This repository contains the taxonomic and functional annotation of the IGC database.</p> <p><strong>full_taxonomy_MetaHIT99.tsv </strong>: Taxonomic assignment of proteins from IGC database with the sequence aligner DIAMOND against the non-redundant NCBI database, with an e-value threshold of 10<sup>-4</sup> </p> <p><strong>KEGG89_IGC_hs99.table</strong> : Functional annotation of proteins from IGC database with KEGG resource with an e-value threshold of 10<sup>-5</sup>, a bit-score threshold of 60 and using the sensitive mode of DIAMOND</p>
Gene annotation of the Fhb1 locus on the assembly of bread wheat variety Norin 61
<p>In the areas with wet climate of Eastern Asia, Fusarium head blight (FHB) is a major threat to bread wheat production. A source of FHB resistance (<em>Fhb1</em>) was identified in the Asian wheat germplasm and through classical breeding it was introduced in several varieties (https://doi.org/10.1186/s40066-017-0139-z ). The molecular determinant was identified as a deletion in an histidine-rich calcium-binding-protein gene on chromosome 3BS. (https://doi.org/10.1038/s41588-019-0426-7). The allele is common in many East Asia wheat varieties, but not in the reference assembly Chinese Spring (CS). </p> <p>The whole-genome assembly of the Japanese variety Norin 61 allowed to confirm the sequence and structure of the haplotype surrounding <em>Fhb1</em>. Given the low amount of sequence conservation with CS at the locus, we noticed that the annotation based on projections of CS gene models (https://doi.org/10.1038/s41586-020-2961-x) did not identify all genes in the Norin 61 haplotype.</p> <p>To describe the complete set of coding regions in the <em>Fhb1</em> allele, we de novo annotated the Norin 61 ~340 kb <em>Fhb1</em> region with homology- and ab initio-based evidence. MAKER v2.31.9 was run on the Norin 61 genomic interval, with the Uniprot Liliopsida proteome, and the annotation from https://doi.org/10.1038/s41586-020-2961-x. Augustus was run with wheat as a species, and the output was parsed removing models that had >40% similarity over >50% of their length to TE proteins via BLASTP.</p> <p>Our annotation identified 70 protein-coding genes, 50 more than the ones identified by homology only.A deletion in the start codon (third exon) of <em>TaHRC</em> gene was confirmed as the causal mutaiton conferring resistance, and it was present in other vaireties having the same resistance.</p> <p>This resource highlights the importance of an appropriate characterization of the sequence in a non-reference genotype, especially when considering new variants with traits important for modern breeding programs.</p>
Gene and TE annotation - Merenciano 2023
<p>Gene and TE annotation for wild-type strains of D. melanogaster and D. simulans.</p><p>Both genomes were annotated with liftoff v.1.6.3, parameters -a 0.5 -s 0.75 -exclude_partial. For D. melanogaster, we used reference genome from flybase r6.16; and for D. simulans we used ref genome from flybase r2.02</p><p> </p><p>D. melanogaster Tropical region (São José do Rio Preto - Brazil):</p><p>-dmsj23</p><p>-dmsj7</p><p>D. melanogaster Temperate region (Gotheron - France):</p><p>-dmgoth101</p><p>-dmgoth63</p><p> </p><p>D. simulans Tropical region (São José do Rio Preto - Brazil):</p><p>-dssj9</p><p>-dssj27</p><p>D. simulans Temperate region (Gotheron - France):</p><p>-dsgoth31</p><p>-dsgoth613</p>
Gene catalogs and KEGG annotation related to root metagenomic samples
<p><span>Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of </span><span>crop </span><span>root microbiome</span><span>s</span><span>. Combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (</span><span>68.9 % </span><span>from isolates) </span><span>and 1,817 novel species,</span><span> expanding crop root bacterial diversity by </span><span>290.6%</span><span>. The crop root viral genome collection (CRVC) contains 9,736 nonredundant viral genomes, with 1,572 previously unreported genus-level clusters in crop roots. From these data, we identified conserved bacterial </span><span>functions</span><span> enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria–virus </span><span>connections</span><span> in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture. </span></p> <p> </p> <p>The gene sets of 14 datasets are available under this accession.</p>
Assembly-mapped metaproteomics gene annotations from Columbia River hyporheic sediments
<p>Annotations for the full set of genes that recruited unique peptides from the Columbia River hyporheic zone sediments manuscript.</p>
Gene annotation of complete genome sequence of Achromobacter sp. strain E1
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The gene structure annotation, gene function annotation and TE annatition files of the Glyphodes pyloalis's genome
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Free cancer gene annotations
<p>Cancer genes annotations from various free sources</p>
The gene structure annotation, gene function annotation and TE annatition files for the Cibotium barometz isolate CiBa-2024 genome
<p>This dataset comprises comprehensive annotation files for the genome of Cibotium barometz (Golden Chicken Fern), isolate CiBa-2024. It includes gene structure predictions, functional annotations, and transposable element (TE) identifications, complementing the chromosome-level genome assembly. The gene structure annotation provides detailed information on predicted gene models, including exon-intron boundaries and coding sequences. Functional annotations offer insights into the potential roles of identified genes, including Gene Ontology (GO) terms, protein domains, and pathway associations. The TE annotation file details the classification and distribution of transposable elements within the genome. These annotations were generated using state-of-the-art bioinformatics tools and databases, offering a valuable resource for researchers studying fern genomics, plant evolution, and the genetic basis of C. barometz's unique biological features, including its medicinal properties. This dataset aims to facilitate further research in comparative genomics, functional studies, and the exploration of fern biology and evolution.</p>
Genome assembly and gene annotations for a Morus alba var. zhenzhubai
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Gene annotations and proteomes for rice-infecting Magnaporthe oryzae isolates
<p>Annotations were performed using FunGAP</p>
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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.