Web Servers

tRNAscan-SE for tRNA predictions (http://lowelab.ucsc.edu/tRNAscan-SE/)
snoscan for C/D box snoRNA predictions (http://lowelab.ucsc.edu/snoscan/)
snoGPS for H/ACA snoRNA predictions (http://lowelab.ucsc.edu/snoGPS/)

Databases

UCSC Archaeal Genome Browser (http://archaea.ucsc.edu)
UCSC Microbial Genome Browser (http://microbes.ucsc.edu)
Genomic tRNA Database (http://gtrnadb.ucsc.edu)
snoRNA Database for Yeast and Archaea (http://lowelab.ucsc.edu/snoRNAdb/)