RNA Accessibility in cubic time 英文参考文献.docVIP

Bernhartetal.AlgorithmsforMolecularBiology2011,6:3 /content/6/1/3 RESEARCH OpenAccess RNAAccessibilityincubictime StephanHBernhart*,UllrikeMückstein,IvoLHofacker Abstract Background:TheaccessibilityofRNAbindingmotifscontrolstheefficacyofmanybiologicalprocesses.Examples arethebindingofmiRNA,siRNAorbacterialsRNAtotheirrespectivetargets.Similarly,theaccessibilityofthe Shine-Dalgarnosequenceisessentialfortranslationtostartinprokaryotes.Furthermore,manyclassesofRNA bindingproteinsrequirethebindingsitetobesingle-stranded. Results:WeintroduceawaytocomputetheaccessibilityofallintervalswithinanRNAsequencein O(n3 )time. Thisimprovesonpreviousimplementationswhereonlyintervalsofonedefinedlengthwerecomputedinthe sametime.Whilethealgorithmisinthesameefficiencyclassassamplingapproaches,theresults,especiallyifthe probabilitiesgetsmall,aremuchmoreexact. Conclusions:OuralgorithmsignificantlyspeedsupmethodsforthepredictionofRNA-RNAinteractionsandother applicationsthatrequiretheaccessibilityofRNAmolecules.Thealgorithmisalreadyavailableintheprogram RNAplfoldoftheViennaRNApackage. Background intermolecularduplexδGint andthecostofopeningthe TheimportanceofRNAwithinlivingcellshasbeenrea- binding sites δGopen. The opening energy can be com- lized in the last two decades. RNA provides a layer of puted from the accessibility, defined as the probability regulation in eukaryotes, e.g. via miRNA, but also in pu that the binding site is unpaired in equilibrium, via prokaryotes via small RNAs (sRNAs) and riboswitches. δGopen =-RTln(pu). Many of these regulatory functions are mediated by Themostnaiveapproachtocomputetheaccessibility RNAinteractions.Theseinteractionsaremainlyrealized ofacertainstretchofbasesistouseaconstrainedfold- through Watson-Crick orwobble basepairing between ing where no base pairs are allowed within a certain twoRNAmolecules.Fortheinitializationoftheseinter- stretch of bases and dividing the respective restricted actions, a part of the interact