SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation

Abstract

The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).

Complexity of begomovirus and betasatellite populations associated with chilli leaf curl disease in India

“…Using the CLUSTAL W method in SDT v. 1.0 (Muhire et al, 2014) and MEGA5 (Tamura et al, 2011), neighbour-joining phylogenetic dendrograms and percentage pairwise identity of the identified sequences and the representative sequences from the database were generated. For RDP analysis, the begomoviruses were selected according to the criteria followed by George et al (2015) and the sequence accession numbers are listed in Table S4.…”

Phylogenetic and Genome-Wide Pairwise Distance Analysis of the Genus Luteovirus

“…However, for species demarcation, inference from the full length sequences is more meaningful, if considered, since they correspond to biological entities and may represent occurrence of genetic recombination. Pairwise sequence comparison carried out, in this study, using sequence demarcation tool (Muhire et al, 2014), has previously been used for Mastrevirus (Muhire et al, 2013), Curtovirus and more recently for Begomovirus (Brown et al, 2015) of the family Geminiviridae. Sequence based species cutoff alone is accurate and reflects biological differences between viruses belonging to different species (Brown et al, 2015) at least in the case of Begomovirus [Family Geminiviridae] -Bean golden mosaic virus (phloem restricted) and Bean golden yellow mosaic virus (invades mesophyll tissues).…”

“…MUSCLE algorithm (Edgar, 2004) was used to align the sequences, with gap penalties (gap open = -400 and gap extend = 0). Pairwise sequence comparison was also carried out using sequence demarcation tool (Muhire et al, 2014). Maximum Likelihood phylogeny was predicted for the isolates under study that grouped into the genus Luteovirus computed with MEGA 5.1 (Tamura et al, 2011) with best-fit nucleotide substitution (GTR+G) model.…”

Çanakkale ili börülce üretim alanlarında Hıyar mozaik virüsü (Cucumber mosaic virus; CMV)’nün tespiti ve kılıf protein genine göre moleküler karakterizasyonu

“…Daha sonra bu CMV izolatına ait elde edilen konsensus dizi NCBI (National Centre for Biotechnology Information)'dan indirilen diğer CMV izolatlarına ait CP sekans verileri ile birlikte filogenetik ağaçların oluşturulmasında kullanılmıştır (Çizelge 1). Bu amaçla CWP17 CP genlerine ait nükleotid dizileri CLC Main Workbench programında ClustalW ile çoklu dizi karşılaştırması yapılarak birbirleriyle ve dünya izolatlarıyla olan nt ve a.a. düzeyindeki benzerlik oranları tespit edilerek Sequence Demarcation Tool, version 1.2 (SDTv1.2) kullanılarak renklendirilmiş matrix olarak elde edilmiştir (Muhire et al 2014). CWP17 izolatının filogenetik ilişkileri de aynı programda Neighbor-joining ve UPGMA metoduyla kiamura iki algoritması uygulanarak 1000 tekrarlı bootstrap analizi ile belirlenmiştir.…”