miR-Search

mir-search is a pipeline devloped to examine and analyse the role of miRNA target site structure in the context of gene expression

Introduction

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.

mir-search is written in Python 3.8.

The mir-search pipeline consists of 4 modules:

• pymart
• mir-search
• icshape-align
• ggplot-format

pymart:

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.

mir-search:

The mir-search module is used to identify all 6mer, 7mer and 8mer targets of a given micro-RNA

icshape-align:

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:

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

Usage

pymart:

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" />).

mir-search:

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.

icshape-align

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