I have a bunch of (human) Agilent probes (both probe ID and the actual sequence, some custom array), and I would like to get the hgnc gene symbol based on the actual probe sequences, rather than the IDs (I can use the ID to get hgnc gene symbol, but I want to match the actual probe sequence).
What I would like is some CLI way of
- submitting all probes (as a fasta file?)
- getting the hgnc gene symbol for each probe based on the best alignment
with either a way of specifying an alignment threshold before, or getting hgnc gene symbol and some alignment quality score so I can prune out the bad hits.
I can do all of the above interactively, but the probes are more than 200K, so I need an automated CLI way.