KATSS - K-mer Analysis Tools for Sequence and Structure

A C package containing programs to analyze RNA-protein interaction.

Introduction

KATSS is a collection of C programs designed for the analysis of RNA sequences, particularly focusing on RNA-protein interactions. The package includes two main programs: kstruct and ikke, each tailored for specific analyses.

The tools allow you to:

• Calculate the motif of RNA-binding proteins
• Determine the secondary motifs
• Statistically determine enrichments without a control dataset
• Predict the binding preference of a protein

Table of Contents

1. Installation
2. Executable Program
3. Example Usage
4. License

Installation

KATSS uses CMake to install the programs. In order to compile from source, the following dependencies are required:

• ViennaRNA, for RNA structure prediction
• zlib OR ISA-L, to read from compressed files
• CMake >= 3.9.0, the build toolchain used by katss

Quick Start

Once you download the project, you can simply do the following:

cd katss
cmake -B build && cmake --build build
cmake --build build --target install

Note: This will install the binaries into the default system path, which is typically /usr/local/bin.

User-dir Installation

One issue you might encounter with the previous installation is that it might require root privileges. In case you do not have root privileges in your computer, you can specify the installation location to a place you have write access to by using the -DCMAKE_INSTALL_PREFIX flag as such:

cmake -DCMAKE_INSTALL_PREFIX=/your/preferred/path -B build && cmake --build build
cmake --build build --target install

Ensure that the specified path is included in your system's PATH environment variable to execute the binaries conveniently from any location.

Executable Programs

The KATSS package includes the following executable programs:

Program	Description
ikke	Compute enriched motifs in RNA-sequences
kstruct	Predict k-mer preference in base-pair interactions in protein-bound RNA

To get more information about a program, run them with the --help or --detailed-help flag as such:

ikke --detailed-help

Example Usage

kstruct

kstruct -i control_sequences.fastq.gz -b bound_sequences.fastq.gz -o output.csv -k 3

ikke

ikke -t test_seqs.fastq.gz -c ctrl_seqs.fastq.gz -o output -dt --kmer=6 --iterations=10

License

This project is licensed under GNU General Public License v3.0. See the LICENSE file for full details.