| BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm272 Sequence analysis RNA Sampler: a new sampling based algorithm for common RNA (2008) | |||||||||||||||
Abstract | |||||||||||||||
| Motivation: Non-coding RNA genes and RNA structural regulatory motifs play important roles in gene regulation and other cellular functions. They are often characterized by specific secondary structures that are critical to their functions and are often conserved in phylogenetically or functionally related sequences. Predicting common RNA secondary structures in multiple unaligned sequences remains a challenge in bioinformatics research. Methods and Results: We present a new sampling based algorithm to predict common RNA secondary structures in multiple unaligned sequences. Our algorithm finds the common structure between two sequences by probabilistically sampling aligned stems based on stem conservation calculated from intrasequence base pairing probabilities and intersequence base alignment probabilities. It iteratively updates these probabilities based on sampled structures | |||||||||||||||
Publication details | |||||||||||||||
| |||||||||||||||