典型文献
Identification of Non-Coding RNAs Based on Alignment-Free Features in Crassostrea gigas (Pacific Oyster) Transcriptome
文献摘要：
Non-coding RNAs (ncRNAs) play important roles in the regulation of many biological processes, such as transcription initiation and epigenetic modifications that occur after transcription and development. Several novel transcripts have been identified via high-throughput sequencing. However, identifying ncRNAs among the transcripts of novel species using alignment-based fea- tures is difficult. Thus, developing a fast and accurate method based on alignment-free features to identify ncRNAs among novel transcripts is necessary. In this study, we proposed a new approach, namely, coding potential prediction based on alignment-free fea- tures (CPAF), to identify ncRNAs among a large number of candidates. CPAF used four types of features: Fickett score; Hexamer score; composition, transition, and distribution features; and modified k-mer. From the results, CPAF performed better than previous state-of-the-art methods in predicting ncRNA transcripts, with particular reference to small ncRNAs. Finally, we applied CPAF to identify ncRNAs in Pacific oyster transcripts. Our approach identified more ncRNAs than other previously used methods.
文献关键词：
中图分类号：
作者姓名：
CHAI Wenjing;SONG Kai
作者机构：
School of Mathematics and Statistics,Qingdao University,Qingdao 266071,China
文献出处：
引用格式：
[1]CHAI Wenjing;SONG Kai-.Identification of Non-Coding RNAs Based on Alignment-Free Features in Crassostrea gigas (Pacific Oyster) Transcriptome)[J].中国海洋大学学报（自然科学英文版）,2022(06):1633-1640
A类：
CPAF,Fickett,Hexamer
B类：
Identification,Non,Coding,Based,Alignment,Free,Features,Crassostrea,gigas,Pacific,Oyster,Transcriptome,coding,ncRNAs,play,important,roles,regulation,many,biological,processes,such,transcription,initiation,epigenetic,modifications,that,occur,after,development,Several,novel,transcripts,have,been,identified,via,high,throughput,sequencing,However,identifying,among,species,using,alignment,difficult,Thus,developing,fast,accurate,free,features,necessary,In,this,study,proposed,new,approach,namely,potential,prediction,large,number,candidates,used,four,types,score,composition,transition,distribution,modified,From,results,performed,better,than,state,methods,predicting,particular,reference,small,Finally,applied,oyster,Our,more,other,previously
AB值：
0.533958
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