Assembly and Analysis of Parvovirus Genomes

For assembly of the parvovirus genomes, the contigs showing significant BLASTx similarity to parvoviruses were selected [45 (link)]. The contigs with consensus sequence length >500 bp were subjected to further analysis, where the individual contig was used as reference for mapping to the raw data of its original barcode using the Low Sensitivity/Fastest parameter in Geneious (RRID:SCR_010519) [45 (link)]. Those prolonged contigs that had the major nonstructural protein and structural protein, as well as some contigs that had only a nonstructural protein, were included in this study. The contigs that had only a putative nonstructural protein are not shown in this study. Splice sites were also detected using Neural Network of the Berkeley Drosophila Genome Project. The search for protein homologies was made by BLAST programs at the NCBI website (http://www.ncbi.nlm.nih.gov/Blast.cgi) against the nonredundant protein database, and alignment of protein sequences was performed using the Mega 10.2.2 (RRID:SCR_000667).

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Dai Z., Wang H., Wu H., Zhang Q., Ji L., Wang X., Shen Q., Yang S., Ma X., Shan T, & Zhang W. (2023). Parvovirus dark matter in the cloaca of wild birds. GigaScience, 12, giad001.

Publication 2023

Consensus sequence Drosophila Genome Mega 10 Parvoviruses Protein Sensitivity Sequences alignment

Corresponding Organization : Chinese Academy of Agricultural Sciences

Other organizations : Yancheng Third People's Hospital, Affiliated Hospital of Nantong University, Nantong University, Harbin University, Qinghai Institute for Endemic Diease Prevention and Control

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Variable analysis

independent variables

Contigs showing significant BLASTx similarity to parvoviruses

dependent variables

Contigs with consensus sequence length >500 bp
Contigs that had the major nonstructural protein and structural protein
Contigs that had only a nonstructural protein

control variables

Mapping of individual contigs to the raw data of their original barcode using the Low Sensitivity/Fastest parameter in Geneious
Searching for protein homologies using BLAST programs at the NCBI website against the nonredundant protein database
Alignment of protein sequences using the Mega 10.2.2

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

Annotations

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