Using purine skews to predict genes in AT-rich poxviruses
Date
2005-02-18
Authors
Da Silva, Melissa
Upton, Chris
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: Clusters or runs of purines on the mRNA synonymous strand have been found in
many different organisms including orthopoxviruses. The purine bias that is exhibited by these
clusters can be observed using a purine skew and in the case of poxviruses, these skews can be
used to help determine the coding strand of a particular segment of the genome. Combined with
previous findings that minor ORFs have lower than average aspartate and glutamate composition
and higher than average serine composition, purine content can be used to predict the likelihood
of a poxvirus ORF being a "real gene".
Results: Using purine skews and a "quality" measure designed to incorporate previous findings
about minor ORFs, we have found that in our training case (vaccinia virus strain Copenhagen), 59
of 65 minor (small and unlikely to be a real genes) ORFs were correctly classified as being minor.
Of the 201 major (large and likely to be real genes) vaccinia ORFs, 192 were correctly classified as
being major. Performing a similar analysis with the entomopoxvirus amsacta moorei (AMEV), it was
found that 4 major ORFs were incorrectly classified as minor and 9 minor ORFs were incorrectly
classified as major. The purine abundance observed for major ORFs in vaccinia virus was found to
stem primarily from the first codon position with both the second and third codon positions
containing roughly equal amounts of purines and pyrimidines.
Conclusion: Purine skews and a "quality" measure can be used to predict functional ORFs and
purine skews in particular can be used to determine which of two overlapping ORFs is most likely
to be the real gene if neither of the two ORFs has orthologs in other poxviruses.
Description
BioMed Central
Keywords
Citation
DaSilva and Upton. Using purine skews to predict genes in AT-rich poxviruses. BMC Genomics 2005, 6:22