Hi Christos, why not post your progress here?

Good idea to blast the Arabidopsis translated exons (Protein fragments) against the translated Aquilegia TCs.  The protein matches will be much better, then with the coordinated of the mRNA matching a coding exon you can check if there is a SNP.

Here is the file from Willem with the double hit SNPs in the EST contigs AQSNP_for_Genaissance.fasta.zip