Richard Durbin suggested trying this variation of the query:
select a from s in class sequence where s = "Em:AC104662", a in s->DNA_homol
The result is intermediate, 4-5 seconds.
> select a from a in object ("sequence", "Em:AC104662")->DNA_homol
>> takes < 1 sec, whereas
>> select a from s in class sequence, a in s->DNA_homol where s = "Em:AC104662"
>> takes 110 sec.