mir-search is a pipeline devloped to examine and analyse the role of miRNA target site structure in the context of gene expression
mir-search is a pipeline devloped as part of my MSc research project. It combines RNA-Seq data and SHAPE-Seq data in order to visualise the role that mRNA secondary structure has on miRNA mediated gene regulation.
Furthermore the pipeline implements the ViennaRNA Package to calculate the minimum free energy (MFE) structure for specified target sites, to facilitate comparison to SHAPE-Seq data.
mir-search is written in Python 3.8.
The mir-search pipeline consists of 5 modules:
- pymart
- mir-search
- icshape-align
- ggplot-format
- rnafold
The pymart module allows you to download 3'UTR sequence data directly from biomart for a given subset of genes. It also cleans the 3'UTR data to remove unavailible sequence data and prepares it for direct use within mir-search module.
The mir-search module is used to identify all 6mer, 7mer and 8mer targets of a given micro-RNA
The icshape-align module takes the output from the mir-search module as well as SHAPE-Seq data and extracts structure scores for each nucleotide in the target region
ggplot-format is a helper module that takes the output from the mir-search or icshape-align module and parses the data in a way that allows for direct plotting with the R library, ggplot2
rna-fold is a module that implements the ViennaRNA Package to calculate the minimum free energy (MFE) structure for target site specified in the mir-search output. This takes the target site locations +/- a flanking region and pipes them to the RNAfold stdin, runs RNAfold and then captures the stdout.
The stdout includes: minimum free energy (MFE) structure, MFE structure in dot-bracket notation and its free energy to as well as the partition function and the base pairing probability matrix.
Usage: python mir-search pymart -i "genelist" - o "output" -a
Note: The genelist should be a csv file with the first column the ensembl gene IDs
template.xml contains the xml request string. This currently obtains 3'UTR sequences (specified via: <Attribute name = "3utr" />).
Usage: python mir-search mir-search -i -m input_mir_name input_utr.fasta
Note: The -m flag specifies the input micro RNA name as seen on mirbank.
Usage: mir-search icshape-align -s icshape_output -t mir_search_output -u UTR file -f 0
Note: The -f flag specifies the length of the flanking region to read
Usage: mir-search rnafold -t mir_search_output -u UTR file -f 30
Note: The -f flag specifies the length of the flanking region to read `