#bioinformatics #rna #secondary-structure

bin+lib consalifold

Prediction Tool for RNA Consensus Secondary Structures to Consider RNA Pairwise Structural Alignments

5 releases

Uses old Rust 2015

0.1.4 Jul 19, 2021
0.1.3 Feb 17, 2021
0.1.2 Feb 15, 2021
0.1.1 Nov 13, 2020
0.1.0 Jul 13, 2020

#95 in Science

32 downloads per month

MIT license

6.5MB
3K SLoC

Python 2.5K SLoC // 0.0% comments Rust 470 SLoC

Prediction Tool for RNA Consensus Secondary Structures to Consider RNA Pairwise Structural Alignments

Installation

This project is written mainly in Rust, a systems programming language. You need to install Rust components, i.e., rustc (the Rust compiler), cargo (the Rust package manager), and the Rust standard library. Visit the Rust website to see more about Rust. You can install Rust components with the following one line:

$ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

The above installation is done by Rustup, and Rustup enables to easily switch a compiler in use. As ConsAlifold's dependencies, you need to install ViennaRNA and LocARNA-P (if you wish to use instead of ConsProb). You can install ConsAlifold as follows:

$ RUSTFLAGS='--emit asm -C target-feature=+avx -C target-feature=+ssse3 -C target-feature=+mmx' cargo install consalifold # AVX, SSE, and MMX enabled for rustc (another example: RUSTFLAGS='--emit asm -C target-feature=+avx2 -C target-feature=+ssse3 -C target-feature=+mmx -C target-feature=+fma')

Check if you have installed ConsAlifold properly as follows:

$ consalifold # Its available command options will be displayed.

By the following Python script, you can reproduce the figures shown in the paper describing ConsAlifold's principle:

$ cd scripts
$ ./run_all.py # Please install python packages required to this reproduction. Saved figures will appear at the "../assets/images" directory.

Author

Heartsh

License

Copyright (c) 2018 Heartsh
Licensed under the MIT license.

Dependencies

~27MB
~199K SLoC