Trim Silva_seed into v1-3

Dear mothur users,
I am trying to trim the silva seed to keep only the v 1-3 region to use later in aligning 454 sequences. i did a bit of exercise and i figured that 1046 to 8405 is the region of interest. i used 27F/519R.
a second question, if i remove.lineage also to keep only the bacteria i.e. create Silva_Seed_v1-3_bacteria.align, do i still need to remove lineage down the stream?

many thanks

OA

if i remove.lineage also to keep only the bacteria i.e. create Silva_Seed_v1-3_bacteria.align, do i still need to remove lineage down the stream?

Probably. To remove chloroplasts, mitochondria, and unknowns.