I have updated the Blast server slightly, following Heidi's request:
When using BlastN or TBlastX vs. genomic scaffolds (LSalAtl2s masked and unmasked, but not "Everything L. Salmonis) the result page will list all genomic features that overlap with the location of the hit. This is very handy to test e.g. if primers or other short sequences hit the correct gene.

Details: this has not been implemented by making a new database with the gene sequences only. Instead the overlaps are computed from the annotation on the fly. This has several advantages:
- you will still get all the hits, even if they don't overlap anything
- the list is dynamic, if features are added to the annotation in the database, they will be visible immediately
- we could make it more configurable in the future, e.g. by including flanking regions of variable size to genes or restrict listing of overlaps to certain types

Note: this update has no effect for other databases, such as Protein databases or ESTs where it wouldn't make sense.

Typical output would look like this:

>LSalAtl2s1000

Length = 153,939
Score = 32.2 bits (16), Expect = 0.28
Identities = 16/16 (100%), Frame = +1 / -1

overlapping features:

mRNA EMLSAT00000000001
gene EMLSAG00000000001
polypeptide polypeptide-auto769988
exon EMLSAE00000000002
microarray_oligo IMR_012781_PI392524217
microarray_oligo IMR_012782_PI392524217
microarray_oligo CUST_21138_PI425553006
microarray_oligo CUST_21139_PI425553006
microarray_oligo CUST_21140_PI425553006
EST_match zslaa0_008212.z1.scf
cDNA_match gi|306564360|gb|HO687952.1|HO687952
cDNA_match gi|306564360|gb|HO687952.1|HO687952
cDNA_match zslaa0_008212.z1.scf

Query: 1     AAGGATGGTAAATGAA 16
             |||||||||||||||| 
Sbjct: 33886 AAGGATGGTAAATGAA 33871