Bioinformatics analysis of SARS coronavirus genome polymorphism

Background: We have compared 38 isolates of the SARS-CoV complete genome. The main goal was twofold: first, to analyze and compare nucleotide sequences and to identify positions of single nucleotide polymorphism (SNP), insertions and deletions, and second, to group them according to sequence similarity, eventually pointing to phylogeny of SARS-CoV isolates. The comparison is based on genome polymorphism such as insertions or deletions and the number and positions of SNPs. Results: The nucleotide structure of all 38 isolates is presented. Based on insertions and deletions and dissimilarity due to SNPs, the dataset of all the isolates has been qualitatively classified into three groups each having their own subgroups. These are the A-group with "regular" isolates (no insertions / deletions except for 5' and 3' ends), the B-group of isolates with "long insertions", and the C-group of isolates with "many individual" insertions and deletions. The iso...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Gordana Pavlovic-Lazetic, Nenad S. Mitic, Milos V. Beljanski
• Keywords: BMCBI 2004, Isolates, Single Nucleotide Polymorphism, SNPs