Functional RNA Database (fRNAdb) is a database service that hosts a large collection of non-coding transcripts including annotated/un-annotated sequences from H-inv database, NONCODE, and RNAdb. A set of computational sequence analyses are performed over these registered sequences. The analyses include RNA secondary structure motif discovery, EST support, finding cis-regulatory elements, sequence homology search, etc. The fRNAdb provides an efficient interface to help users filter out particular transcripts that match their own criteria to sort out functional RNA candidates.