miRanda在线预测miRNA靶基因
简介
miRanda是一种检测基因组序列中miRNA潜在靶位点的算法。当前版本:v3.3a
miRanda is an algorithm for the detection of potential microRNA target sites in genomic sequences
两步策略:1,在查询的miRNA序列和mRNA 3'UTR序列间进行动态规划局部比对。这一比对过程基于序列互补(而不是序列一致性)打分;2,基于第一步获得的高分比对结果(sc参数控制),使用RNAlib(来自ViennaRNA包)评估比对的热力学稳定性。最终能量小于阈值(en参数控制)的结果作为最终结果。
源码见官网!
数据说明
1,fasta格式的miRNA序列
2,fasta格式的mRNA 3'UTR序列,或者fasta格式的lncRNA序列,circRNA序列等目标序列
结果文件中:'|'表示完全匹配,':'表示G:U配对,' '表示错配。
参考文献
A.J. Enright, B. John, U. Gaul, T. Tuschl, C. Sander, D.S. Marks; (2003) MicroRNA targets in Drosophila; Genome Biology 5(1):R1.
输入miRNA序列 |
>hsa-miR-27b
UUCACAGUGGCUAAGUUCUGC |
输入mRNA 3'UTR序列 |
>Bcl3
GACGGATGGGGGGGCAGACCCGGACTCATGAGGAGGGGCCTCCCTGCCCTGT
GGGGACCACTCTTCTGGAAACTGTGAGGACCTTGTTCTGCTTCCCCCCGCCC
AATCCTCGGGACCAGGTTTTGCACCAAGGCACATGCACATACTACTGAGCACA
GATCCTCCCAATCGCGCCCCTTGCCCAGGACTCTCAGCCCCCACTTAATCTCA
GGCACCCAGGTTCCCTGTCTGGAATCCACCAGATACTCAATTCTTTGAGTGGA
GGAACCAAAGGACAGCCAGCCTCTCCTCTGCCACCCTCCACCCTGAGGGACCC
AGAGAAACAGAGGGGTCTGGGAGGGCATTGATCACAGTGTAAATTATTAGGTT
TGGGTCAGATTTCTTTTGTAATAAACTATTTTTGTATCAT |
输出 |
|
如何引用?
建议直接写网址。4600+篇
google学术,3900+篇
知网学术
正式引用:Tang D, Chen M, Huang X, Zhang G, Zeng L, Zhang G, Wu S, Wang Y.
SRplot: A free online platform for data visualization and graphing. PLoS One. 2023 Nov 9;18(11):e0294236. doi: 10.1371/journal.pone.0294236. PMID: 37943830.
方法章节:Heatmap was plotted by https://www.bioinformatics.com.cn (last accessed on 10 Dec 2024), an online platform for data analysis and visualization.
致谢章节:We thank Mingjie Chen (Shanghai NewCore Biotechnology Co., Ltd.) for providing data analysis and visualization support.