So, I need to predict which miRNAs bind to which genes. My supervisor aksed me to check for every possibilities in every part of mRNA, not only 3' UTR. Before, I found tools to predict the binding site of mRNAs in mRNAs only from its 3'UTR.
What I have right now is RNA-seq and Exome-seq data. I imagine, I only need to do some alignment (complementary) for miRNA sequence which I downloaded from miRBase and the RNA-seq reads. Is there any tools out there to do this? I think this function is similar to NCBI BLAST.
Details on my data: I'm working with human data. I used Ensembl human reference Hg 38.80. My data is for cancer-normal pair experiment from NCBI GEO consists of 7 pair of RNASEQ data and 8 pair of Exome seq data.
After doing some research, I think I found that probably I can use FASTA from cDNA from Ensembl. In that case, I will have full sequence per gene transcript. I also have the miRNA FASTA file. I will only need to search the pattern of the miRNA in the cDNA sequence. Is it possible and meaningful? What tools is available to align FASTA to FASTA file?