Hard for any language to beat:

ClassMethod makeComplement(d As %String) As %String
{
 q $tr(d,"ATGC","TACG")
}

Not great around edge cases, but this passes the tests at least (and might beat a $find-based approach since it avoids set commands):

ClassMethod findShort(s) As %Integer
{
 f i=1:1 ret:$locate(s,"(^| )\w{"_i_"}( |$)") i
}

If the thing you're working with is actually some sort of configuration data then this is probably a good approach. If not then building your own integration to transmit the data is probably better.