DEVELOPMENT OF BROADLY AMPLIFYING
REAL TIME PCRs FOR DETECTION AND QUANTIFICATION OF RETROVIRAL NUCLEIC ACID
Jonas Blomberg, Anna Forsman, Patric
Jern, Dmitrijis Ushameckis, Poya Tababat-Khani
Section of Virology, Department of
Medical Sciences, Academic Hospital Uppsala, Sweden
To better understand the evolution of
the human genome, the many thousands of human endogenous retroviral sequences
(HERVs) need to be enumerated and characterized. An expert system,
“Retrospector”, which does this in an automated fashion has been
created. The system first searches for presence of conserved amino acid
motifs, then tests if they come in a logical order, at logical distances from
each other. The system then uses the motif information to attempt a
translation of the gag pro pol and env genes, taking into account similarity to
known retroviral proteins and absence of stop codons. The system can
operate batchwise, and can cover large stretches on its own. The system,
and some results from the human genome, will be presented.
Poster
