Fast and reliable prediction of noncoding RNAs

By Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler. Proc. Natl. Acad. Sci. USA, 2005

737 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/7f201defb7dc5347e36823d5b9b49c2ec71a53a0

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Citations in the corpus

ViennaRNA Package 2.0 (2011, neutral): “The non-coding RNA gene finder RNAz [95,96], the snoRNA detector snoReport [97], and RNAstrand [98], a tool that predicts the reading direction of structured RNAs from a multiple sequence alignment, combine thermodynamic properties computed with RNAlib functions and a machine learning component.”
Rfam: updates to the RNA families database (2008, neutral): “The rate of discovery of new RNA families is accelerating rapidly, facilitated by advancements in new sequencing technologies (12, 13) and targeted computational screens (14) (15) (16) (17) .”
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. (2012, positive): “To this end, we investigated how well certain features—including the average pairwise sequence identity (APSI), the structural conservation index (SCI) (Washietl et al. 2005a), and the STAR score—correlate with alignment quality on a benchmark set of 10-way (reference) alignments from the Rfam datab”
The Landscape of long non-coding RNA classification (2015, neutral): “A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript Category Abbreviation Reference Specific Examples Expressed Satellite Repeats [164] Non-coding RNA driven by promoters within repeats vlincRNAs, NASTs [29, 76] Vlinc_21, vlinc_185, vlinc_377, vlinc_500 [29] Polypurine-re”
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (2008, positive): “We also chose LaRA as an alternative pairwise alignment method, because it shows a characteristic pattern of the SPS score for pairwise alignment (N = 2) and it has a remarkably high structure conservation index [9,46,47].”
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering (2007, neutral): “employed to detect ncRNAs with evolutionarily conserved se condary structures [7, 8, 9, 10, 11, 12].”
PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach (2011, neutral): “On all datasets we use two measurement to evaluate the performance of each alignment scheme: (1) sum-of-pairs score (SPS), which represents the percentage of correctly aligned bases; (2) structure conservation index (SCI) [45] that measures the degree of conservation of the consensus secondary struc”
RNAstructure: software for RNA secondary structure prediction and analysis (2010, positive): “Novel types of ncRNAs can be found in genomes on the basis of folding stability [40-42].”
Comparative analysis of the complete genome sequence of the plant growth–promoting bacterium Bacillus amyloliquefaciens FZB42 (2007, neutral): “The resulting (multiple) sequence alignments were scored using RNA”
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006, neutral): “This evolutionary signal can be exploited for comparative identiﬁcation of fRNAs [6–12].”
A benchmark of multiple sequence alignment programs upon structural RNAs (2005, neutral): “RNA structure analysis (1–5), RNA homology search (6,7), non-coding RNA (ncRNA) detection (8,9) and RNA-based phylogenetic inference (10,11)].”
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007, neutral): “Several comparative approaches to RNA gene identification have been developed 6,7,65 that recognize their characteristic properties: compensatory double substitutions of paired nucleotides (for example, A .”
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. (2008, neutral): “RNAz uses multiple genome alignments to predict regions that contain thermodynamically stable and conserved RNA secondary structures (Washietl et al. 2005b).”
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities (2008, neutral): “These include the programs QRNA [38], RNAz [39], and EvoFOLD [40].”