ambivirus_extended_data
Artem Babaian edited this page Aug 22, 2022
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4 revisions
Preprint: Extant hybrids of RNA viruses and viroid-like elements. (Forgia, Navarro et al., 2022)
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ambi_rdrp_id90.fa: 422 Ambivirus RdRp sequences; centroids from 90% amino acid identity clustering -
ambi_genome_id90.fa: 612 Ambivirus putative complete genome sequences, centroids from 90% nucleotide identity clustering
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ambi_palm_msa.fa: Multiple sequence alignment of ambi-palmprints for constructing phylogeny -
ambi_tree.newick: Tree file for ambivirus phylogeny
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dvr5.cmRibozyme CM models for "deltavirus", "hairpin", several "hammerhead", "twister" and "Varkud Satellite" motifs. Used to search the ~200K metagenome/metatranscriptome libraries in the SRA.
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viroid-like_circles.tar.gz: Tar file containing ~32K circular RNA (viroid-like elements) sequences and metadata identified in theRDVAdataset.
All data is cc0 following INSDC/Serratus Data policies
- Accessing Serratus Data
- Data Types
- Sequence References
- Running Serratus
- Finding Novel Viruses (tutorials)
- Papers using Serratus
- Containers
- Summarizer usage
- Cloud Budgeting
- Data Policy
- Serratus Annotation
- Serratus Assembly
- FLOM reference
- Proteome guided assembly for high divergence low coverage genomes
- PRICE de novo assembly
- Taxonomy case study of misannotated Genbank entry
- Taxonomy prediction
- Tree placement and taxonomy data
- Design of nucleotide summarizer scoring and-depth estimates
- Cov-phylogenetic-tree-quality-by-monophylicity
- Running a Treesearch
- Finding-transfer---recombination-events-in-the-Spike-protein
- Serratus SQL Database Management
- Trees-and-alignments-for-Ribovirus-orders-and-families
- Viral-contigs-containing-RdRP