From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs 英文参考文献.docVIP

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From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs 英文参考文献.doc

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From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs 英文参考文献

Review FromStructurePredictiontoGenomicScreensforNovel Non-CodingRNAs JanGorodkin1,2*,IvoL.Hofacker1,3 * 1Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, Denmark, 2Division of Genetics and Bioinformatics, IBHV UniversityofCopenhagen,Frederiksberg,Denmark,3DepartmentofTheoreticalChemistry,UniversityofVienna,Wien,Austria largely unstructured [16]. The repertoire of ncRNAs is rapidly expanding and RNA-seq sequencing techniques, in combination Abstract:Non-codingRNAs(ncRNAs)arereceivingmore and more attention not only as an abundant class of genes, but also as regulatory structural elements (some located in mRNAs). A key feature of RNA function is its structure. Computational methods were developed early with computer methods, are expected to give rise to a general expansionoftheRNAuniverse.TheseRNAfamiliesarecollected intheRfamdatabase[17]intheformofstructuralalignmentsand consensusstructures.Inanumberofcases,suchasSRPRNAsand forfoldingandpredictionofRNAstructurewiththeaim tmRNAs [18], Rfam is based on pre-existing curated RNA of assisting in functional analysis. With the discovery of structural alignments from specialized databases. This important moreandmorencRNAs,ithasbecomeclearthatalarge resource is also often used to construct and test RNA structure fraction of these are highly structured. Interestingly, a largepartofthestructureiscomprisedofregularWatson- Crick and GU wobble base pairs. This and the increased predictiontools[7]. The size variation of ncRNAs is extreme, ranging from *20 amount of available genomes have made it possible to employ structure-based methods for genomic screens. The field has moved from folding prediction of single sequences to computational screens for ncRNAs in genomic sequence using the RNA structure as the main characteristicfeature.Whereasearlymethodsfocusedon energy-directedfoldingofsinglesequences,comparative analysis based on structure preserving changes of base pairshasbeen