{"title":"利用序列基序特征可以实现准确的植物MicroRNA预测","authors":"M. Yousef, J. Allmer, Waleed Khalifa","doi":"10.4236/JILSA.2016.81002","DOIUrl":null,"url":null,"abstract":"MicroRNAs (miRNAs) are short (~21 nt) nucleotide sequences that are either co-transcribed during the production of mRNA or are organized in intergenic regions transcribed by RNA polymerase II. In animals, Drosha, and in plants DCL1 recognize pre-miRNAs which set themselves apart by their characteristic stem loop (hairpin) structure. This structure appears important for their recognition during the process of maturation leading to functioning mature miRNAs. A large body of research is available for computational pre-miRNA detection in animals, but less within the plant kingdom. For the prediction of pre-miRNAs, usually machine learning approaches are employed. Therefore, it is necessary to convert the pre-miRNAs into a set of features that can be calculated and many such features have been described. We here select a subset of the previously described features and add sequence motifs as new features. The resulting model which we called MotifmiRNAPred was tested on known pre-miRNAs listed in miRBase and its accuracy was compared to existing approaches in the field. With an accuracy of 99.95% for the generalized plant model, it distinguishes itself from previously published results which reach an average accuracy between 74% and 98%. We believe that our approach is useful for prediction of pre-miRNAs in plants without per species adjustment.","PeriodicalId":69452,"journal":{"name":"智能学习系统与应用(英文)","volume":"08 1","pages":"9-22"},"PeriodicalIF":0.0000,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"17","resultStr":"{\"title\":\"Accurate Plant MicroRNA Prediction Can Be Achieved Using Sequence Motif Features\",\"authors\":\"M. Yousef, J. Allmer, Waleed Khalifa\",\"doi\":\"10.4236/JILSA.2016.81002\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"MicroRNAs (miRNAs) are short (~21 nt) nucleotide sequences that are either co-transcribed during the production of mRNA or are organized in intergenic regions transcribed by RNA polymerase II. In animals, Drosha, and in plants DCL1 recognize pre-miRNAs which set themselves apart by their characteristic stem loop (hairpin) structure. This structure appears important for their recognition during the process of maturation leading to functioning mature miRNAs. A large body of research is available for computational pre-miRNA detection in animals, but less within the plant kingdom. For the prediction of pre-miRNAs, usually machine learning approaches are employed. Therefore, it is necessary to convert the pre-miRNAs into a set of features that can be calculated and many such features have been described. We here select a subset of the previously described features and add sequence motifs as new features. The resulting model which we called MotifmiRNAPred was tested on known pre-miRNAs listed in miRBase and its accuracy was compared to existing approaches in the field. With an accuracy of 99.95% for the generalized plant model, it distinguishes itself from previously published results which reach an average accuracy between 74% and 98%. We believe that our approach is useful for prediction of pre-miRNAs in plants without per species adjustment.\",\"PeriodicalId\":69452,\"journal\":{\"name\":\"智能学习系统与应用(英文)\",\"volume\":\"08 1\",\"pages\":\"9-22\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2016-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"17\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"智能学习系统与应用(英文)\",\"FirstCategoryId\":\"1093\",\"ListUrlMain\":\"https://doi.org/10.4236/JILSA.2016.81002\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"智能学习系统与应用(英文)","FirstCategoryId":"1093","ListUrlMain":"https://doi.org/10.4236/JILSA.2016.81002","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Accurate Plant MicroRNA Prediction Can Be Achieved Using Sequence Motif Features
MicroRNAs (miRNAs) are short (~21 nt) nucleotide sequences that are either co-transcribed during the production of mRNA or are organized in intergenic regions transcribed by RNA polymerase II. In animals, Drosha, and in plants DCL1 recognize pre-miRNAs which set themselves apart by their characteristic stem loop (hairpin) structure. This structure appears important for their recognition during the process of maturation leading to functioning mature miRNAs. A large body of research is available for computational pre-miRNA detection in animals, but less within the plant kingdom. For the prediction of pre-miRNAs, usually machine learning approaches are employed. Therefore, it is necessary to convert the pre-miRNAs into a set of features that can be calculated and many such features have been described. We here select a subset of the previously described features and add sequence motifs as new features. The resulting model which we called MotifmiRNAPred was tested on known pre-miRNAs listed in miRBase and its accuracy was compared to existing approaches in the field. With an accuracy of 99.95% for the generalized plant model, it distinguishes itself from previously published results which reach an average accuracy between 74% and 98%. We believe that our approach is useful for prediction of pre-miRNAs in plants without per species adjustment.