|
Phages are most likely to be the
most abundant biological entity
on the planet. Phage particles are
simple in that all known phages
are comprised of 2 components: 1)
genetic material; and 2) structural
proteins. Despite their simplicity
and abundance, up to 56% (151784/269906)
of phage coding sequences have unknown
function based on the annotations
of coding sequences retrieved by
GenBank queries. As a result, the
use of sequence similarity is not
an effective method of detecting
phage structural proteins from large
amounts of unknown phage sequence
data that is generated by metagenomics.
In addition, phage structural protein
function is challenging to predict
from sequence data because phage
structural proteins possess little
known conserved catalytic sites
or sequence domains. To detect phage
structural protein sequences we
used multiple two layer feed-forward
Artificial Neural Networks (ANN)
that use the Levenberg-Marquardt
supervised learning algorithm with
validation. The trained ANNs correctly
identified viral structural protein
genes with >87% sensitivity and
>80% specificity.
|