Partial index

Hi everyone,

i have a function that looks executes the following command in a while loop in which it iterates through tables (aTable):
FOR rec in EXECUTE 'SELECT count(a.allele_1) as c from aTable a INNER JOIN map_table b on(a.snp_id=upper(b.snp_id)) WHERE NOT a.allele_1=a.allele_2 and b.gene=something

Unfortunately this command leads to 4 minutes of execution for 15 tables of which each has around 3 Million tuples. I have a partial index on the expression where not allele_1=allele_2 and one on snp_id.
Here is the explain i get for the above mentioned command:
Aggregate (cost=229621.08..229621.09 rows=1 width=16)

-> Merge Join (cost=496.29..229361.10 rows=103991 width=16)

Merge Cond: (("outer".snp_id)::text = "inner"."?column2?")

-> Index Scan using idx_snpid_pt1 on snp_allel_chr_11pt1 a (cost=0.00..212667.07 rows=2875580 width=29)

Filter: ((allele_1)::text <> (allele_2)::text)

-> Sort (cost=496.29..496.63 rows=138 width=13)

Sort Key: upper((b.snp_id)::text)

-> Bitmap Heap Scan on snps_map b (cost=2.48..491.38 rows=138 width=13)

Recheck Cond: ((gene)::text = 'FN5'::text)

-> Bitmap Index Scan on idx_snps_map_gene (cost=0.00..2.48 rows=138 width=0)

Index Cond: ((gene)::text = 'FN5'::text)
As you can see the partial index is not used. So, does anyone have a suggestion on how to increase the performance of the queries.

Thanks
Chris

Christian Rengstl M.A.
Klinik und Poliklinik für Innere Medizin II
Kardiologie - Forschung
Universitätsklinikum Regensburg
B3 1.388
Franz-Josef-Strauss-Allee 11
93053 Regensburg
Tel.: +49-941-944-7230