sequence alignment - (Jun/13/2012 )

Hi
I have to align genomic sequence of HKT1 with mRNA to design primers for the exons. I am sure you’ve done this, what are the freeware available? Thanks a lot
Cheer
Chandima

NCBI, BLAST, primer3, BLAT

What species? If you already have sequences, such as a shotgun genome sequence and an EST mRNA sequence then go for it, but if you are LOOKING for a rare or non-popular species (platypus)I would try ENSEMBL. They cross-link and reference with NCBI BLAST. Also try the ENA. If you are looking for purely alignment, you might try sequencher as a demo. Primer design is another story. Try NCBI both for the design tool and also as a reference for other people that have already tested primers for your sequence and species.