I have a fasta file of yeast orfs (from the [SGD][1] database) and I need to find out (predict) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous available websites is not an option).

Is [CATH][2] database a place that can give me this info? (so far I struggle to recover anything that can help me from the website but perhaps I am missing something), if not what's the best way/software to go about it? perhaps a piece of code in R or Python.

Surely, these predictions have been done before and there is a database somewhere? -- yeast is too much of an important organism, with a lot of information about its genome.

 [1]: http://www.yeastgenome.org/
 [2]: http://www.cathdb.info/
Okay, so after some searching around I have settled on [s2d][1] software, which might be a bit fiddly to set up but after the initial pain is very easy to use, with nice parseable output.

I've also been recommended [Jpred4][2] -- this one's easy to set up and use.

Both programs offer batch submissions and with s2d I was done with my ~6K proteins in a couple of days (but with some planning I could have done it even faster).

 [1]: http://www-mvsoftware.ch.cam.ac.uk/
 [2]: http://www.compbio.dundee.ac.uk/jpred/