title: LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length.
abstract: BACKGROUND
  Dicer is necessary for the process of mature microRNA (miRNA) formation because the Dicer enzyme cleaves pre-miRNA correctly to generate miRNA with correct seed regions. Nonetheless, the mechanism underlying the selection of a Dicer cleavage site is still not fully understood. To date, several studies have been conducted to solve this problem, for example, a recent discovery indicates that the loop/bulge structure plays a central role in the selection of Dicer cleavage sites. In accordance with this breakthrough, a support vector machine (SVM)-based method called PHDCleav was developed to predict Dicer cleavage sites which outperforms other methods based on random forest and naive Bayes. PHDCleav, however, tests only whether a position in the shift window belongs to a loop/bulge structure.
  
  
  RESULTS
  In this paper, we used the length of loop/bulge structures (in addition to their presence or absence) to develop an improved method, LBSizeCleav, for predicting Dicer cleavage sites. To evaluate our method, we used 810 empirically validated sequences of human pre-miRNAs and performed fivefold cross-validation. In both 5p and 3p arms of pre-miRNAs, LBSizeCleav showed greater prediction accuracy than PHDCleav did. This result suggests that the length of loop/bulge structures is useful for prediction of Dicer cleavage sites.
  
  
  CONCLUSIONS
  We developed a novel algorithm for feature space mapping based on the length of a loop/bulge for predicting Dicer cleavage sites. The better performance of our method indicates the usefulness of the length of loop/bulge structures for such predictions.
authors.affiliation: Laboratory of Mathematical Bioinformatics, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan. houu@kuicr.kyoto-u.ac.jp.
authors.forename: Yu
authors.initials: Y
authors.lastname: Bao
authors.affiliation: Laboratory of Mathematical Bioinformatics, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
authors.forename: Morihiro
authors.initials: M
authors.lastname: Hayashida
authors.affiliation: Laboratory of Mathematical Bioinformatics, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Akutsu
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001499:Bayes Theorem; D053487:DEAD-box RNA Helicases; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000235:genetics* / Q000378:metabolism; D043244:Ribonuclease III / Q000378:metabolism*; D012984:Software; D060388:Support Vector Machine
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases
keywords: Dicer cleavage site; Loop/bulge length; Support vector machine