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ORIGINAL PAPER Sequence analysis Sequence-based heuristics for faster annotation of non-coding RNA families (2005)
| Content Provider | CiteSeerX |
|---|---|
| Author | Ruzzo, Walter L. Salzberg, Steven L. Weinberg, Zasha |
| Abstract | Motivation: Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are auseful statistical tool to findnewmembersofanncRNAgene family ina large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM’s accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. Results: In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that—unlike family-specific solutions—can scale to hundreds of ncRNA families. Availability:Thesource code is available underGNUPublic Licenseat the supplementary web site. Contact: |
| File Format | |
| Publisher Date | 2005-01-01 |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
