Dear friends, I have ~2000 sequences of 60 DNA bases, of different organisms. I need to run a BLAT query on each sequence, in order to get the edge-bases coordinates. Then I would like to use a Get-DNA query (or equivalent) to retrieve the sequence + additional 20 bases on each side.

What is the recommended approach? Is there a specific API I should use? Should I use UCSC/Ensembl?

Thanks a lot in advance.