tRNAs and other stories

[Eddy S./Durbin]

In article <17JUN199307593560 at aardvark.ucs.uoknor.edu> broe at aardvark.ucs.uoknor.edu (Bruce Roe) writes:
  >As for programs to find tRNA genes, there are several
  >available, for Mac's, PC's, VAX's and SUNS.  Tell me what computer
  >they want to use and maybe I can point you to a source for them.

Could you be coerced into posting a summary, with references where
possible?

I was under the impression that searching for secondary structures is
still a fairly open problem. The software I'm aware of for searching
for tRNAs and other RNA molecules is all based on regular
expression-like search engines. This means you have to build a search
pattern by hand (laborious as hell, particularly when you start
wanting to search for something bigger like a group I intron), and you
must specify the conserved positions inflexibly (i.e., you can't
specify probabilities for each position and get an overall score for a
match; you specify base pairs and identities at the conserved
positions, allow your pattern to tolerate some number of mismatches,
and get a yes or no answer whether your pattern matches a sequence).

- Sean Eddy
- Laboratory of Molecular Biology, MRC, Cambridge UK
- sre at mrc-lmb.cam.ac.uk