Computational protocol: Multiple Layers of Chimerism in a Single-Stranded DNA Virus Discovered by Deep Sequencing

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[…] Domain recognition in the CHIV14 RC-Rep protein was performed using HHpred () against the PFAM database. Structural modeling was performed using Modeller v9.9 (), as described previously (). X-ray structures of tomato bushy stunt virus (TBSV; PDB ID: 2TBV), melon necrotic spot virus (MNSV; PDB ID: 2ZAH), carnation mottle virus (CMV; PDB ID: 1OPO), and turnip crinkle virus (TCV; PDB ID: 3ZXA) were used as templates. Sequence of CHIV14 CP was aligned with the corresponding sequences of TBSV, MNSV, CMV, and TCV, and the resultant alignment was used to build a three-dimensional model of the putative CP of CHIV14. The initial model was optimized through multiple rounds of loop refinement with MODELLER. The stereochemical quality of the model was then assessed with ProSA-web (). ProSA-web quality (Z) score for the CHIV14 model was calculated to be −5.83, which is similar to the Z-scores determined for the template structures (TBSV, −5.18; MNSV, −6.26; CMV, −6.06; TCV, −3.39). The percent sequence identity between the CHIV CPs was mapped onto the structural model of the CHIV14 CP.Sequences of the previously described CHIVs () were retrieved as GenBank-formatted files from Dryad Digital Repository, http://dx.doi.org/10.5061/dryad.19m2k (last accessed March 4, 2015). For phylogenetic analysis, protein sequences were aligned using PROMALS3D () and columns with low information content were removed from the alignment (alignments are available from the authors upon request). All alignments generated in the course of this study are available from the authors upon request. Maximum-likelihood phylogenetic analysis was carried out using PhyML 3.1 (), with the Jones–Taylor–Thornton model of amino acid substitutions, including a gamma law with four substitution rate categories. […]

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