Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs

By Elena Rivas, Sean R. Eddy. Bioinform., 2000

330 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c8f1d738b591197da0dbd55cf1ff9afdda047b64

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In Molecular Biology

Citations in the corpus

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. (2001, neutral): “The mutual incorporation of the different criteria narrowed down the list were shown to be insufficient for distinguishing nontrans-lated RNAs from random sequences [24], the computa-of candidates and resulted in the prediction of a total of 24 putative sRNA genes (Table 1).”
Non–coding RNA genes and the modern RNA world (2001, background): “Previous attempts to develop ncRNA gene-finders that work on a single genome sequence have been stymied by the apparent lack of much significant statistical signal in ncRNA”
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences (2004, background): “For this reason, the dinucleotide bias in RNA sequences is considered to be important for the predicted MFE and several authors have pointed out the importance of taking into account the dinucleotide distributions when randomizing sequences (Workman and Krogh, 1999; Rivas and Eddy, 2000).”
Computational identification of noncoding RNAs in E. coli by comparative genomics. (2001, neutral): “[3].”
Noncoding RNA gene detection using comparative sequence analysis (2001, methodology): “We have previously explored one RNA genefinding approach with very limited success [12].”
Fast and reliable prediction of noncoding RNAs (2005, positive): “Although thermodynamic stability is not significant alone, it still can be used as valuable diagnostic feature since functional RNAs are indeed more stable than random sequences to some degree [32, 27].”
CONTRAfold: RNA secondary structure prediction without physics-based models (2006, methodology): “As the authors themselves note, QRNA underperforms compared to standard folders, highlighting the difficulty of building SCFGs on par with energy-based methods [18].”
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006, background): “The development of computational methods that can efﬁciently identify fRNAs by comparative genomics has been hampered by the fact that fRNAs often exhibit only weakly conserved primary-sequence signals [5].”