Computational protocol: Whole-Genome Analysis of a Novel Fish Reovirus (MsReV) Discloses Aquareovirus Genomic Structure Relationship with Host in Saline Environments

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Protocol publication

[…] The nucleotide sequences and deduced amino acid sequences were analyzed using the EditSeq program (DNASTAR 5.0). Homology searches of nucleic acid and protein databases were performed using BLAST at the National Centre for Biotechnology Information server. Multiple sequence alignments were performed using Clustal X 1.83 program, and sequence identities were calculated using the Clusta W method in the MegAlign program (DNASTAR 5.0). Transmembrane helices were predicted using TMHMM 2.0 []. The coiled regions in MsReV NS87 protein were predicted using the COILS Server (http://embnet.vital-it.ch/software/COILS_form.html). The equivalent genome segments and proteins between MsReV and two other representative aquareoviruses, SMReV and GCReV-109, were analyzed and shown in a schematic diagram. [...] Phylogenetic analysis was performed based on the alignment of the concatenated sequences of seven structural proteins that are conserved in all sequenced aquareoviruses (). The seven structural proteins from 12 other aquareoviruses were rearranged as continuous amino acid sequences with the same order as MsReV. The concatenated protein sequences were then aligned with the Clustal X 1.83 program, and phylogenetic tree was constructed using the neighbor-joining method with 1000 bootstrap replicates in MEGA5 software []. GenBank accession numbers of the aquareovirus sequences used for analysis were shown in . […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Micropterus salmoides, Scophthalmus maximus, Ctenopharyngodon idella