RTM-align

Official code for RTM-align: an improved RNA alignment tool with enhanced short sequence performance via post-standardization and fragment alignment

Benchmarking results demonstrated that RTMalign significantly improved classification accuracy (from 68% to 98%) on the challenging short-pairs dataset compared to RNA-align. Furthermore, it maintained robust performance for longer RNAs, achieving consistent results regardless of RNA length.

This program is developed based on RNA-align: https://zhanggroup.org/RNA-align/download.html

Getting Started

Dataset

All dataset considered can be found at https://doi.org/10.6084/m9.figshare.25903405.v2

Install

To install RTM-align, follow these steps:

1. compiler preparation

requirement for compiling RTM-align: gcc(12.2.0 in our environment), python(3.10.x in our environment for visualizing fragment alignment only)

2. clone the repo

git clone https://github.com/BEAM-Labs/RTM-align.git
cd RTM-align/code
make RTMalign

The "-static" flag in MakeFile should be removed on Mac OS, which does not support building static executables.

Use RTM-align

Briefly, to alignment two single-chain structures (1.pdb and 2.pdb), enter the following:

./RTMalign 1.pdb 2.pdb

If want to visualize fragment alignment (remember to change filex and filey in run.sh):

bash ./run.sh

You can run the program without arguments to obtain a brief instruction. Full document for all available options can be obained by:

./RTMalign -h