利用简并K元组策略高效鉴定microRNA前体 - CSDN文库

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"使用简并K元组或Kmer策略鉴定microRNA前体" 这篇研究论文探讨了如何利用简并K元组（degenerate K-tuple）或Kmer策略来鉴定microRNA（miRNA）的前体。miRNA在基因表达调控中起着至关重要的作用，它们通过与靶标mRNA结合，参与转录后基因表达的调控。因此，正确识别真实的miRNA前体（pre-miRNA）对于理解miRNA的功能和在miRNA为基础的疗法中的应用至关重要。简并K元组和Kmer是生物信息学中常用的序列分析工具。K元组是指长度为K的DNA或RNA序列片段，而简并K元组则允许在K元组的某些位置上存在多种可能的核苷酸，这增加了搜索空间的多样性，有助于捕捉到更广泛的序列特征。Kmer策略则是在一个序列中寻找特定长度K的连续子串，这些子串可能包含特定的序列模式，对于识别具有相似结构或功能的分子非常有用。在本研究中，作者开发了一种新的预测器，旨在快速有效地识别miRNA前体。这个预测器利用简并K元组和Kmer策略来捕获pre-miRNA的结构和序列特性，这些特性包括茎环结构、保守区域和可能的剪切位点等。通过对大量已知pre-miRNA和非pre-miRNA序列的数据分析，研究人员训练和优化了模型，以提高预测的准确性和特异性。文章经过多次修改和审稿，最终于2015年被接受发表。关键词包括“microRNA前体”，表明该研究聚焦于miRNA生命周期的关键步骤，即pre-miRNA的识别。这项工作对于深入理解miRNA的生物学功能，以及在疾病诊断和治疗中潜在的应用，如miRNA靶向疗法，具有重要的理论和实践意义。这项研究提供了一个创新的方法，利用计算方法加速和改进miRNA前体的鉴定，这对于miRNA研究领域是一个有价值的贡献。通过这种策略，科学家们可以更高效地筛选出具有潜在生物学活性的pre-miRNA，从而推动miRNA相关研究的进步。

Identiﬁcation of microRNA precursor with the degenerate K-tuple

or Kmer strategy

Bin Liu

a,b,c,

n

, Longyun Fang

a

, Shanyi Wang

a

, Xiaolong Wang

a,b

, Hongtao Li

d

,

Kuo-Chen Chou

c,e

a

School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China

b

Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China

c

Gordon Life Science Institute, Boston, MA 0478, USA

d

Wendeng Marine Environmental Monitoring Station, Station Oceanic Administration Wendeng, Weihai, Shandong, China

e

Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia

HIGHLIGHTS



microRNA (miRNA) plays an important role in gene expression.



Identiﬁcation of real pre-miRNAs is important miRNA-based therapy.



A novel predictor was developed for fast and effectively identifying miRNA.

article info

Article history:

Received 16 July 2015

Received in revised form

21 August 2015

Accepted 24 August 2015

Available online 9 September 2015

Keywords:

MicroRNA precursor

True pre-miRNA

False pre-miRNA

Degenerate Kmer

deKmer web-server

Long-range effect

abstract

The microRNA (miRNA), a small non-coding RNA molecule, plays an important role in transcriptional and

post-transcriptional regulation of gene expression. Its abnormal expression, however, has been observed

in many cancers and other disease states, implying that the miRNA molecules are also deeply involved in

these diseases, particularly in carcinogenesis. Therefore, it is important for both basic research and

miRNA-based therapy to discriminate the real pre-miRNAs from the false ones (such as hairpin

sequences with similar stem-loops). Most existing methods in this regard were based on the strategy in

which RNA samples were formulated by a vector formed by their Kmer components. But the length of

Kmers must be very short; otherwise, the vector's dimension would be extremely large, leading to the

“high-dimension disaster” or overﬁtting problem. Inspired by the concept of “degenerate energy levels”

in quantum mechanics, we introduced the “degenerate Kmer” (deKmer) to represent RNA samples. By

doing so, not only we can accommodate long-range coupling effects but also we can avoid the high-

dimension problem. Rigorous jackknife tests and cross-species experiments indicated that our approach

is very promising. It has not escaped our notice that the deKmer approach can also be applied to many

other areas of computational biology. A user-friendly web-server for the new predictor has been

established at http://bioinformatics.hitsz.edu.cn/miRNA-deKmer/, by which users can easily get their

desired results.

& 2015 Elsevier Ltd. All rights reserved.

1. Introduction

MicroRNAs (miRNAs) are small single-strand and non-coding

RNAs (ncRNAs), which play important roles in gene regulation by

targeting messenger RNAs (mRNAs) for cleavage or translational

repression (Fig.1). Their lengths are about 17–25 nt (Lopes et al.,

2014). The miRNAs are also involved in many important biological

processes, such as affecting stability, translation of mRNAs, and

negatively regulating gene expression in post-transcriptional

processes. Therefore, it is fundamentally important to identify the

real pre-miRNAs from the false ones. Unfortunately, it is difﬁcult to

Contents lists available at ScienceDirect

journal homepage: www.elsevier.com/locate/yjtbi

Journal of Theoretical Biology

http://dx.doi.org/10.1016/j.jtbi.2015.08.025

0022-5193/& 2015 Elsevier Ltd. All rights reserved.

n

Correspondence to: Harbin Institute of Technology Shenzhen Graduate School,

HIT Campus Shenzhen University Town, Xili, Shenzhen 518055, China.

Tel.: þ 86 0755 2603 3283.

E-mail addresses: bliu@insun.hit.edu.cn (B. Liu),

dragoncloudest@gmail.com (L. Fang), wangshanyiwsy@gmail.com (S. Wang),

wangxl@insun.hit.edu.cn (X. Wang), lht760@126.com (H. Li),

kcchou@gordonlifescience.org (K.-C. Chou).

Journal of Theoretical Biology 385 (2015) 153–159

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