Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

Bahir, Iris; Fromer, Menachem; Prat, Yosef; Linial, Michal

Proteins for all organisms were collected from UniProt (Apweiler et al, 2004) . Virus proteins were collected from ViralZone (http://www.expasy.ch/viralzone, coordinated by UniProt/SwissProt), which holds 314 reference strain viruses that belong to 80 families and 291 genera. ViralZone provides reviewed data that cover molecular information (shape, genome and replication mode, and capsomer composition), epidemiological data, cell tropism, and host range. Each genus is specified by a manually selected representative (in some cases, 41). All viruses are classified into seven classes: (I) double-stranded DNA viruses, (II) single-stranded DNA viruses, (III) double-stranded RNA viruses, single-stranded RNA viruses with positive and negative sense (IV, V, respectively), (VI) positive sense single-stranded RNA viruses that replicate through a DNA intermediate and double-stranded DNA viruses that replicate though a single-stranded RNA intermediate (VII). Fragmented proteins and polyproteins were filtered out. Coding sequences were collected from EMBL through an SRS querying system that links UniProt proteins to their respective EMBL coding sequences. As one protein is often associated with multiple sequences, we extracted all data as mapped by EMBL to UniProt ID. This collection of virus proteins in UniProt covers B13 000 proteins that are reviewed (SwissProt) and additionally B730 000 from a non-reviewed TrEMBL resource.