I agree with the second best practice but feel that the code example is still somewhat hard to read. I like to format select statements as follows:
select distinct
clo.clone_id,
clc.collection_name,
clo.source_clone_id,
clo.image_clone_id,
lib.library_name,
lib.vector_name,
lib.host_name,
loc.plate,
loc.plate_row,
loc.plate_column,
clo.catalog_number,
clo.acclist,
clo.vendor_id,
clc.value,
lib.species,
seq.cluster
from clone clo
inner join collection clc on clo.collection_id = clc.collection_id
inner join library lib on clo.library_id = lib.source_lib_id
inner join location loc on clo.clone_id = loc.clone_id
inner join sequence seq on clo.clone_id = seq.clone_id
where clc.short_collection_type='cDNA'
and clc.is_public = 1
and clo.active = 1
and clo.no_sale = 0
and seq.cluster in (select cluster from master_xref_new where
type='CLONE' and id='LD10094')