Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV029213 GenBank Accession BK066745
Subfamily unclassified Parvoviridae Genus unclassified Parvoviridae
Species Parvovirus homo4417 Sequence Length 4417
Definition MAG TPA_asm: Parvovirus homo4417 isolate Parvo4417 genomic sequence. Submission Date 2024-02-23
Strain Name Parvo4417 Sampling Date 2015
Sampling Country Venezuela Location Venezuela
Submitted By Buck,C.B., Welch,N., Belford,A.K., Varsani,A., Pastrana,D.V., Tisza,M.J. and Starrett,G.J. Submitting Institution Lab of Cellular Oncology, National Cancer Institute, Building 37 Room 4118, Bethesda, MD 20892, USA
Original Host Homo sapiens Sample Type feces
Standardized Host Name Homo sapiens Host Tax Rank species
Standardized Host Class Mammalia Standardized Host Order Primates
Environmental Origin - N/A - Reagent Origin - N/A -
Number Reagent/Consumables Purpose PMID/Url Reference
1 Diamond 2.0 Used for scanning unassembled read sets for small DNA tumor virus hallmark protein sequences. 38712252 View Related Publication
2 SRA Toolkit 2.9.6 (fastq-dump module) Used for initial sequence downloads with settings to split files and gzip.
3 SRA Toolkit 3.0.3 (fasterq-dump module) Used for recent assembly efforts to download reads faster.
4 Seqtk Used to sample 50 million read pairs.
5 fastp Used to quality-trim reads.
6 Megahit 1.2.9 Used to assemble trimmed reads with a specified minimum contig length.
7 CLC Genomics Workbench 22 Used for importing de novo-assembled contig sequences and converting them into BLAST databases.
8 Cenote Taker 2 Used for virus genome detection and gene annotation.
9 Cenote Taker 3 Used for auto-annotation of virus groups outside the scope of the current survey.
10 MacVector 18 Used for compiling annotations and displaying maps.
11 HHpred Used for protein structure prediction analysis.
12 Phyre2 Used for protein structure prediction.
13 Dali Used for structural comparisons using AlphaFold2 or RoseTTAfold predictions.
14 EMBOSS getorf Used for analyzing protein sequence clusters.
15 EFI-EST Used for enzyme function discovery and metabolic pathway analysis.
16 PhyML Used for inferring phylogenetic trees.
17 KnotInFrame Used for predicting programmed -1 ribosomal frameshift slippery sequences.
18 Cytoscape Used for visualizing network analyses of viral gene content.
19 FigTree software Used for viewing phylogenetic trees.