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47 results for “fasta”
Alphafold decoys on CASP15 target Fasta Files
<p>This contains the decoys along with the results produced by alphafold2 when run on a subset of CASP15 Fasta Files</p>
DNA sequences of transgenes detected via environmental DNA (raw ABI files, processed FASTA files, and reference alignments)
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Alignment of mitogenome sequences (FASTA file) for a paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies
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Populations genomics of deep-sea hydrothermal vent copepod Stygiopontius lauensis: from raw fasta files to filtered vcf file
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Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
<p><span><span><span><span><span><span><span><span><span><span><span>Litter-decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.</span></span></span></span></span></span></span></span></span></span></span></p>
NCBI Nt (Nucleotide) database FASTA file from 2017-10-26
<p>This FASTA file is the NCBI Nt (Nucleotide) database (public domain) used for holistic metagenomic screening of ancient DNA data at the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History. We offer here the FASTA file used to construct MALT databases (https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/), which are generally too large for uploading. Please see each relevent publications that use the database for MALT database construction commands.</p> <p>NCBI does not retain older versions of this database which is why this has been uploaded here. It was downloaded on 2017-10-26 12:39 from: ftp://ftp-trace.ncbi.nih.gov/blast/db/FASTA/nt.gz. The NCBI Nt database is released into the public domain as per https://www.ncbi.nlm.nih.gov/home/about/policies/.</p> <p> </p>
FASTA 16s gene sequencing files for Control points for design of taxonomic composition in synthetic human gut consortia
<p>FASTA file output from Illumina MiSeq. Processed tally files (reads / species used to calculate relative abundances) are available in the other Zenodo repository listed in the key resources table, under ~ BC###/rawData/tallyfile.xlsx</p>
FASTA file of sequences of identified proteins in Anastrepha ludens reproductive tissues
<p>Seminal fluid proteins (Sfps) modify female phenotypes and have wide-ranging evolutionary implications on fitness in many insects. However, in the Mexican fruit fly, <em>Anastrepha ludens</em>, a highly destructive agricultural pest, the functions of Sfps are still largely unknown. To gain insights into female phenotypes regulated by Sfps, we used nano liquid chromatography mass spectrometry to conduct a proteomic analysis of the soluble proteins from reproductive organs of <em>A. ludens</em>. The proteins predicted to be transferred from males to females during copulation were 100 proteins from the accessory glands, 69 from the testes, and 20 from the ejaculatory bulb, resulting in 141 unique proteins after accounting for redundancies from multiple tissues. These 141 included orthologs to <em>Drosophila melanogaster</em> proteins involved mainly in oogenesis, spermatogenesis, immune response, lifespan, and fecundity. In particular, we found one protein associated with female olfactory response to repellent stimuli (Scribble), and two related to memory formation (aPKC, Shibire). Together, these results raise the possibility that <em>A. ludens</em> Sfps could play a role in regulating female olfactory responses and memory formation and could be indicative of novel evolutionary functions in this important agricultural pest.</p>
ML intro course - TSS exercise FASTA file
<p>The input file needed to go through the TSS exercise in Day 3 of the ML intro course hosted by HeaDS at the University of Copenhagen, Denmark.</p> <p>You can find the course material here: <a title="here" href="https://github.com/Center-for-Health-Data-Science/IntroToML/tree/main">https://github.com/Center-for-Health-Data-Science/IntroToML/tree/main</a></p>
the transcriptome GTFs, FASTA and SQANTI reports for short-read assembled isoforms, long-read assembled isoforms and our assembled isoforms
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FASTA or Tabular Feature Retriever galaxy workflow example output
<p>FASTA Feature Retriever and Tabular Feature Retriever are galaxy workflow that retrieves features(like genes) in fasta or tabular format using .bed and genome .fasta as input</p> <p>input data derived from:</p> <ol> <li><a href="https://solgenomics.net/" target="_blank" rel="noopener">solgenomics.net</a></li> <li><a title="mycocosm" href="https://mycocosm.jgi.doe.gov/Fusso1/Fusso1.home.html" target="_blank" rel="noopener">mycocosm</a></li> </ol>
fasta for screening of lncRNA
<p>fasta for screening of lncRNA</p>
Lepidoptera caterpillars barcodes in FASTA format
<p>The dataset contains COI barcodes of Lepidoptera caterpillars collected from a subtropical forest in Jiangxi, China.</p>
JG-based FASTA index for bwa-mem2
<p>This dataset contains the JG-based index files for bwa-mem 2. We created these with <em>bwa-mem index</em> command using jg.2.1.0.fa(<a href="https://jmorp.megabank.tohoku.ac.jp/downloads/tommo-jg2.1.0-20211208">https://jmorp.megabank.tohoku.ac.jp</a>). As it takes much memory to execute the command, we prepared this dataset.</p>
Human genome fasta file from ensembl (GRCh38 v109)
<p>Human genome fasta file from ensembl (GRCh38 v109), <span>corresponds to GenBank Assembly ID </span><span>GCA_000001405.28</span></p>
Lepidoptera caterpillars barcodes in FASTA format
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Tumour suppressor genes fasta files for orthologous groups and hierarchical orthologous groups
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Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
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FASTA file of sequences of identified proteins in Anastrepha ludens reproductive tissues
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Combined alignment fasta file used for the phylogenetic analysis of Micropsalliota
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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.