如何用targetScan miRanda RNAhybrid预测lncRNA和circRNA的靶向miRNA

targetScan

需要准备两个文件，一个miRNA序列种子文件和lncRNA UTR序列文件。文件格式如下：

#miRNA文件格式 miR_9606_info.txt
#MiRBase ID Seed+m8 Species ID
hsa-miR-9500    AGGGAAG 9606
hsa-miR-8485    ACACACA 9606
hsa-miR-8088    CUCGGUA 9606
hsa-miR-8087    AAGACUU 9606
hsa-miR-8086    GCUAGUC 9606
hsa-miR-8084    AAUACUA 9606

# lncRNA UTR文件格式 SEMA3B.fa
SEMA3B-AS1  9606    AACCCCAGCTCCAGGGGCTCAGCAGGCAAAGGGAATCACTGAGTGGGGGCACCACCCGTGGACTCCAATATCTCAACCTCTCCCTCCACAGGTTGGAGGTGGGAGGAACAACCCCCACCAAACCCAGAGCCGAAAACTGAGGGAGTTTTACAGACAGGACGGAGCTCCTGCACCTCGGAGCCTCAGTTGGGAATGACCTGGGGTCTTGTCCTGAAGCTGAGTCTGGTGAACGTGCCCCATTTGTAACATGAGGGGTACTTCTCTGGAGGGACTGTATGTTGACAGTGGCAGAGTGGAGCCCTGAAGTCCACCTGAGTGAATATACCAGGGCTTGAGAAAAAAAAAAAAAAAAAAAAA

脚本可从targetScan下载，是个perl脚本，用之前需要安装Perl.

perl ../targetscan_70.pl miR_9606_info.txt SEMA3B.fa target_Results.txt

miRanda

也要准备上述两个文件，但是格式有所不同。文件格式如下：

# miRNA文件格式  miRNA9606.fa
>hsa-miR-9500
AAGGGAAGAUGGUGACCAC
>hsa-miR-8485
CACACACACACACACACGUAU
>hsa-miR-8088
CCUCGGUACUGGAAAGGGGUA

# lncRNA UTR文件格式   SEMA3B.fa
>SEMA3B-AS1
AACCCCAGCTCCAGGGGCTCAGCAGGCAAAGGGAATCACTGAGTGGGGGCACCACCCGTGGACTCCAATATCTCAACCTCTCCCTCCACAGGTTGGAGGTGGGAGGAACAACCCCCACCAAACCCAGAGCCGAAAACTGAGGGAGTTTTACAGACAGGACGGAGCTCCTGCACCTCGGAGCCTCAGTTGGGAATGACCTGGGGTCTTGTCCTGAAGCTGAGTCTGGTGAACGTGCCCCATTTGTAACATGAGGGGTACTTCTCTGGAGGGACTGTATGTTGACAGTGGCAGAGTGGAGCCCTGAAGTCCACCTGAGTGAATATACCAGGGCTTGAGAAAAAAAAAAAAAAAAAAAAA

miRanda本地文件可从github下载，解压之后按照README文件编译，安装好之后在src目录下的miranda即可执行，最好在windows的linux子系统操作：

./configure --prefix=/path/to/install
sudo make install
#此处只按照默认参数提取可以匹配的miRNA，要限制匹配条件,可以参考说明书
# /mnt/d/R/UTR/miRanda-1.0b/miRanda-1.0b/src/miranda -h
/mnt/d/R/UTR/miRanda-1.0b/miRanda-1.0b/src/miranda miRNA9606.fa SEMA3B.fa | grep '^>>'|sed  's/^M//g'| sed 's/>>//g' >miRanda_SEMA3B_final_res.txt
# ^M即是Ctrl+C+M

RNAhybrid

输入文件格式跟miRanda是一样的，可从github下载，解压编译后可用。

/mnt/d/R/UTR/RNAhybrid/rnahybrid/src/RNAhybrid -c -p 0.05 -s 3utr_human -t SEMA3B.fa -q miRNA9606.fa |awk -F ":" '{print $1"\t"$3}'|uniq >RNAhybrid_results.txt

# RNAhybrid的选项参数如下
options:
  -b <number of hits per target>
  -c compact output
  -d <xi>,<theta>
  -f helix constraint
  -h help
  -m <max targetlength>
  -n <max query length>
  -u <max internal loop size (per side)>
  -v <max bulge loop size>
  -e <energy cut-off>
  -p <p-value cut-off>
  -s (3utr_fly|3utr_worm|3utr_human)
  -g (ps|png|jpg|all)
  -t <target file>
  -q <query file>

将三个结果用R取交集:

setwd("D:\\R\\UTR\\SEMA3B")
RNAhybrid<-read.table("RNAhybrid_results.txt",header = F,sep = "\t",stringsAsFactors = F)
miRanda<-read.table("miRanda_SEMA3B_final_res.txt",header = F,sep = "\t",stringsAsFactors = F)
target<-read.table("target_Results.txt",header = T,sep = "\t",stringsAsFactors = F)
unique(intersect(RNAhybrid[,2],intersect(target[,2],miRanda[,1])))

"hsa-miR-8077"     "hsa-miR-8071"     "hsa-miR-7847-3p" 
"hsa-miR-7160-5p"  "hsa-miR-7114-5p"  "hsa-miR-7109-5p" 
"hsa-miR-6861-5p"  "hsa-miR-6807-5p"  "hsa-miR-6798-3p" 
"hsa-miR-6794-3p"  "hsa-miR-6777-3p"  "hsa-miR-6776-5p" 
"hsa-miR-6765-5p"  "hsa-miR-6760-3p"  "hsa-miR-6756-5p" 
"hsa-miR-6752-5p"  "hsa-miR-6842-5p"  "hsa-miR-6751-5p" 
"hsa-miR-6803-5p"  "hsa-miR-6749-3p"  "hsa-miR-6739-3p" 
"hsa-miR-6728-3p"  "hsa-miR-6514-3p"  "hsa-miR-5192"    
"hsa-miR-5190"     "hsa-miR-5001-3p"  "hsa-miR-4769-3p" 
"hsa-miR-4763-5p"  "hsa-miR-4739"     "hsa-miR-4756-5p" 
"hsa-miR-4733-3p"  "hsa-miR-4726-3p"  "hsa-miR-6792-3p" 
"hsa-miR-4667-3p"  "hsa-miR-4663"     "hsa-miR-4469"    
"hsa-miR-4459"     "hsa-miR-4447"     "hsa-miR-4472"    
"hsa-miR-5699-3p"  "hsa-miR-6133"     "hsa-miR-4301"    
"hsa-miR-6791-5p"  "hsa-miR-4685-3p"  "hsa-miR-3940-5p" 
"hsa-miR-4507"     "hsa-miR-3934-5p"  "hsa-miR-3692-5p" 
"hsa-miR-3198"     "hsa-miR-3173-5p"  "hsa-miR-6799-3p" 
"hsa-miR-3158-3p"  "hsa-miR-3156-3p"  "hsa-miR-3138"    
"hsa-miR-6875-5p"  "hsa-miR-3120-5p"  "hsa-miR-2467-5p" 
"hsa-miR-1910-5p"  "hsa-miR-1470"     "hsa-miR-1289"    
"hsa-miR-1275"     "hsa-miR-1269b"    "hsa-miR-1260a"   
"hsa-miR-1249-5p"  "hsa-miR-6797-5p"  "hsa-miR-1238-3p" 
"hsa-miR-1225-3p"  "hsa-miR-764"      "hsa-miR-760"     
"hsa-miR-632"      "hsa-miR-623"      "hsa-miR-564"     
"hsa-miR-532-3p"   "hsa-miR-520a-5p"  "hsa-miR-512-5p"  
"hsa-miR-505-3p.2" "hsa-miR-505-3p.1" "hsa-miR-491-5p"  
"hsa-miR-486-3p"   "hsa-miR-370-3p"   "hsa-miR-330-5p"  
"hsa-miR-204-5p"   "hsa-miR-211-5p"   "hsa-miR-193b-5p" 
"hsa-miR-150-5p"   "hsa-miR-146b-3p"  "hsa-miR-125a-3p"