CMfinder - a covariance model based RNA motif finding algorithm

By Zizhen Yao, Zasha Weinberg, W. L. Ruzzo. Bioinform., 2006

379 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/e392cceec9e5cb88ee983002a760e7589f66d9cc

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In Molecular Biology

Citations in the corpus

Revealing protein–lncRNA interaction (2015, methodology): “The already mentioned MEMERIS [49], CMfinder [84], RNApromo [85], StructRED [86], the algorithm by Li and collaborators [87], RNAcontext and RBPmotif [88, 89], GraphProt [90] and Zagros [91] are all tools that use, with different strategies and to different extent, secondary structure information to”
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (2008, background): “Since the discovery of functional non-coding RNAs (ncRNAs), the necessity for the incorporation of secondary structural information into a multiple RNA alignment has been recognized, and many efforts are being made toward this goal [2-14].”
A fast structural multiple alignment method for long RNA sequences (2008, methodology): “proposed an algorithm based on covariance models (CMfinder) [23], and Hamada et al.”
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline (2007, methodology): “For each conserved domain, the collected sequences of potential UTRs were given as input to CMfinder (6) version 0.”
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. (2012, methodology): “Due to its high computational demands, CMfinder has never been applied to whole eukaryotic genomes; for example, in (Torarinsson et al. 2008), it has been applied to the ENCODE region, covering only 1% of the human genome.”
RBPmap: a web server for mapping binding sites of RNA-binding proteins (2014, methodology): “Among them CMfinder (12), which uses a co-variation model for finding motifs in RNA sequences and MEMERIS (13), which is an extension of MEME (14) for finding enriched motifs in RNA sequences, incorporating RNA secondary structure information.”
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure (2008, background): “Currently many algorithms for RNA motif identifications have been proposed [6,32,33].”