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Dataset results
9 results for “protein sequence annotation”
Annotation of Phytozome V12 protein plant sequences using the ragp pipeline for hydroxyproline-rich glycoprotein mining
<p>Hydroxyproline aware annotation of hydroxyproline-rich glycoprotein (HRGP) sequences was performed on sequence data from 62 plant proteomes obtained from Phytozome database (<a href="https://phytozome.jgi.doe.gov/pz/portal.html">https://phytozome.jgi.doe.gov/pz/portal.html</a>, version 12) using the ragp R package (<a href="https://github.com/missuse/ragp">https://github.com/missuse/ragp</a>, version 0.3.0.0001). </p> <p>In each archive a single comma separated value table (.csv) is present along with a README.txt file describing the contents of the corresponding .csv file. The archives are:</p> <p>- phytozome_V12.tar.gz - sequences from 62 plant proteomes (phytozome V12) with a total of 2797062 protein sequences.</p> <p>- phytozome_V12_phobius.tar.gz -<strong> </strong> Signal peptide prediction using Phobius (<a href="http://phobius.sbc.su.se/">http://phobius.sbc.su.se/</a>) on sequences present in phytozome_V12.tar.gz.</p> <p>- phytozome_V12_signalp.tar.gz -<strong> </strong> Signal peptide prediction using SignalP 4.1 (<a href="http://www.cbs.dtu.dk/services/SignalP-4.1/">http://www.cbs.dtu.dk/services/SignalP-4.1/</a>) on sequences present in phytozome_V12.tar.gz.</p> <p>- phytozome_V12_targetp.tar.gz - Signal peptide prediction using TargetP 1.1 (<a href="http://www.cbs.dtu.dk/services/TargetP/">http://www.cbs.dtu.dk/services/TargetP/</a>) on sequences present in phytozome_V12.tar.gz.</p> <p>- phytozome_V12_predict_hyp.tar.gz - Probability of proline hydroxylation for each proline from 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1).</p> <p>- phytozome_V12_maab.tar.gz - Motif and amino acid bias (MAAB) classification of hydroxyproline-rich glycoproteins performed on 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1). The number of predicted hydroxyprolines in each sequence is also indicated (based on predictions provided in phytozome_V12_predict_hyp.tar.gz).</p> <p>- phytozome_V12_scan_ag.tar.gz. - Hydroxyproline aware arabinogalactan motif scan performed on 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1). Hydroxyproline predictions are provided in phytozome_V12_predict_hyp.tar.gz. </p> <p>- phytozome_V12_scan_ag_hmmscan.tar.gz - Detection of domains in a subset of protein sequences which were found to contain arabinogalactan motifs (a subset of phytozome_V12_scan_ag.tar.gz).</p> <p>The list of the 62 plant species is provided in phytozome_V12.tar.gz README.txt.</p> <p>For questions contact mdragicevic@ibiss.bg.ac.rs.</p> <p> </p> <p> </p>
Training data for 'Functional annotation of protein sequences' tutorial (Galaxy Training Material)
<p>The data provided here are part of a Galaxy Training Network tutorial for functional annotation of protein sequences.</p>
Accurate annotation of protein coding sequences with IDTAXA - Training Data
<p>Training data used to test IDTAXA, HMMER, and BLAST performance of classification of amino acid and nucleotide sequences.</p>
Accurate annotation of protein coding sequences with IDTAXA - classification results
<p>Raw classification results generated by IDTAXA, BLAST, and HMMER on a training set scraped from KEGG of > 1.5M sequences. HMMER and BLAST results are also converted into IDTAXA like objects for ease of comparison.</p>
Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation
<p>The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikatis. The detailed description of the datafiles and scripts is provided in the accompanying README.rtf file.</p>
Dataset - Functional annotation for protein sequences
<p>These are the input and output files for the functional annotation of protein sequences workflow tests.</p>
Enhancing Protein Sequence Annotation in Viral Genomics Using Large Language Models and Soft Alignments.
<p>List of 200 most abundant VOG descriptions.</p>
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.
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.
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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.