De novo prediction of structured RNAs from genomic sequences.
Growing recognition of the numerous, diverse and important roles played by non-coding RNA in all organisms motivates better elucidation of these cellular components. Comparative genomics is a powerful tool for this task and is arguably preferable to any high-throughput experimental technology currently available, because evolutionary conservation highlights functionally important regions. Conserved secondary structure, rather than primary sequence, is the hallmark of many functionally important RNAs, because compensatory substitutions in base-paired regions preserve structure. Unfortunately, such substitutions also obscure sequence identity and confound alignment algorithms, which complicates analysis greatly. This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist.
Gorodkin
Jan
J
Section for Genetics and Bioinformatics, IBHV and Center for Applied Bioinformatics, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark. gorodkin@genome.ku.dk
Hofacker
Ivo L
IL
Torarinsson
Elfar
E
Yao
Zizhen
Z
Havgaard
Jakob H
JH
Ruzzo
Walter L
WL
D001483:Base Sequence / Q000235:genetics; D055028:Comparative Genomic Hybridization; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D016678:Genome / Q000235:genetics*; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
D022661:RNA, Untranslated