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40 results for “protein annotation”
Enhancing Protein Sequence Annotation in Viral Genomics Using Large Language Models and Soft Alignments.
<p>List of 200 most abundant VOG descriptions.</p>
Annotation and analysis of the secondary structure elements in the Cytochrome P450 protein family
<p>We collected all currently available structures for proteins in the Cytochrome P450 family and annotated their secondary structure elements using SecStrAnnotator software (https://webchem.ncbr.muni.cz/Wiki/SecStrAnnotator). We used 2nnjA as the template domain for the annotation. Based on these annotations, we analysed the occurrence, length distribution, amino acid sequence, and presence of structural irregularities (β-bulges, 3<sub>10</sub>-helices, π-helices) of each secondary structure element class. We also statistically compared the bacterial vs eukaryotic structures. For the secondary structure element classes with sufficient sequence conservation, the most conserved residue is annotated as the reference residue.</p> <p>Main files:</p> <ul> <li><strong>set_ALL.json</strong> - Set-ALL: list of 1012 protein domains belonging to the Cytochrome P450 family (CATH accession 1.10.630.10 + Pfam accession PF00067, accessed on 7 July 2020, one domain per PDB entry)</li> <li><strong>set_NR.json</strong> - Set-NR: non-redundant list of 183 domains (one domain per UniProt ID)</li> <li><strong>domain_lists_table.tsv</strong> - Overview of Set-ALL and Set-NR and separation into subsets Set-NR-Bact (bacterial), Set-NR-Euka (eukaryotic), Set-NR-Arch (archaeal), Set-NR-Viru (viral)</li> <li><strong>structures/template_2NNJ-template.sses.json</strong> - Manually prepared annotation template (domain 2nnjA)</li> <li><strong>structures/template_2NNJ.cif</strong> - Structure of the template domain (2nnjA)</li> <li><strong>annotations_with_reference_residues_ALL.json, annotations_with_reference_residues_ALL.tsv</strong> - Annotation of secondary structure elements for Set-ALL</li> <li><strong>annotations_with_reference_residues_NR.json, annotations_with_reference_residues_NR.tsv</strong> - Annotation of secondary structure elements for Set-NR</li> <li><strong>aligments_NR</strong> - Multiple sequence alignments for each SSE class (Set-NR)</li> <li><strong>logos_NR</strong> - Sequence logos for each SSE class (Set-NR)</li> <li><strong>plots</strong> - Plots of SSE occurrence, length distribution, contained helix types and beta-bulge occurrence (Set-NR), some plots show the comparison between Set-NR-Bact and Set-NR-Euka</li> <li><strong>statistical_tests.ods</strong> - Comparison of SSE occurrence between Set-NR-Bact and Set-NR-Euka by the test of equal proportions and the Fisher test, comparision of the SSE length by the Kolmogorov-Smirnov test and the two-sample Wilcoxon test</li> </ul>
Domain scanning results for a selected set of high-quality-annotation protein isoforms produced by human transcription factor genes
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Multiple whole genome alignment of 63 Nymphalidae (HAL file, alignment version 1.0), plus protein-coding annotations for each of the species in the hall file.
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Some data for phage protein annotation AI pipeline
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Data from: Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics
The malaria mosquito, Anopheles stephensi, and other mosquitoes modulate their biology to match the time-of-day. In the present work, we used a non-hypothesis driven approach (untargeted proteomics) to identify proteins in mosquito tissue, and then quantified the relative abundance of the identified proteins from An. stephensi bodies. Using these quantified protein levels, we then analyzed the data for proteins that were only detectable at certain times-of-the day, highlighting the need to consider time-of-day in experimental design. Further, we extended our time-of-day analysis to look for proteins which cycle in a rhythmic 24-hour ("circadian") manner, identifying 31 rhythmic proteins. Finally, to maximize the utility of our data, we performed a proteogenomic analysis to improve the genome annotation of An. stephensi. We compare peptides that were detected using mass spectrometry but are 'missing' from the An. stephensi predicted proteome, to reference proteomes from 38 other primarily human disease vector species. We found 239 such peptide matches and reveal that genome annotation can be improved using proteogenomic analysis from taxonomically diverse reference proteomes. Examination of 'missing' peptides revealed reading frame errors, errors in gene-calling, overlapping gene models, and suspected gaps in the genome assembly.
Annotation of Sox family proteins of the snail Lymnaea stagnalis (Mollusca: Pulmonata) using transcriptomic data
<p>This annotation of Sox family proteins of Lymnaea stagnalis snail was performed using transcriptome data from the article:</p> <p>Seppälä, O., Walser, JC., Cereghetti, T. et al. Transcriptome profiling of Lymnaea stagnalis (Gastropoda) for ecoimmunological research. BMC Genomics 22, 144 (2021). https://doi.org/10.1186/s12864-021-07428-1</p> <p>Sox2, Sox14, Sox10 and Sox5/6 were annotated using tBLASTn searches against transcriptome from the article upper. </p>
Computational Analysis, In silico Functional Annotation, and Expression of Recombinant Mycobacterium PE_PGRS Protein Biomarkers
<p>Data set for bioinformatics predictions and expression profiles.</p> <p> </p>
Data from: Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics
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Aegilops tauschii reference genome sequence Aet v5.0 including annotation of small RNAs and reannotation of protein-coding genes
GEO Series GSE169198. Aegilops tauschii. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes
GEO Series GSE60095. Mus musculus; Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing; Other.
Accurate annotation of human protein-coding small open reading frames
GEO Series GSE125218. Homo sapiens. 33 samples. Type: Expression profiling by high throughput sequencing.
Structural annotation of equine protein-coding genes determined by mRNA sequencing
GEO Series GSE21925. Equus caballus. 8 samples. Type: Expression profiling by high throughput sequencing.
Validation of the Swine Protein-Annotated Oligonucleotide Microarray.
GEO Series GSE13095. Sus scrofa. 16 samples. Type: Expression profiling by array.
Functional annotation hypothetical proteins: a world to be explored in drug development in Trypanosomatids - Oligomeric AlphaFold Models
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Excavation of biomarker candidates for the diagnosis of Talaromyces marneffei infection via genome-wide prediction and functional annotation of secreted proteins
GEO Series GSE266975. Talaromyces marneffei. 3 samples. Type: Expression profiling by high throughput sequencing.
Annotating pathogenicity of missense variants from homologous proteins
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High quality de novo long read genome assembly and annotation of resistance protein families for saw toothed grain beetle-Supplementary
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FAPM: Functional Annotation of Proteins using Multi-Modal Models Beyond Structural Modeling
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Nuclear genome annotations, mRNA predictions, and protein predictions
<p>Nuclear genome annotations, mRNA predictions, and protein predictions</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.