TABLE 1.

Genomic regulatory sequences excluded from algorithm optimization in SIVmac239

Sequence(s) excluded	Function during viral replication	Reference(s)
Long terminal repeats	Regulation of transcription, translation, and genome packaging	66
First 300 nucleotides of Gag	Genome packaging in feline immunodeficiency virus- or SIV-derived vector	67, 68
Gag-Pol frameshift	Translation of Pol gene	33
5′ A-rich sequence of Pol	Important for cDNA synthesis during HIV-1 reverse transcription	26
Central polypurine tract and central terminal sequence	Regulation of reverse transcription	68
Rev responsive element	RNA subcellular trafficking	69, 70
Sequences containing donor and acceptor splicing sites	RNA maturation	71–73