This binary provides the CRAST algorithm, a BLAST-like RNA alignment search one.
You can check all the available options by adding the option "-h".
Performance comparison of CRAST with other BLAST-like tools using all 18,185 house mouse ncRNAs/34 human lncRNAs known as homologs to house mouse corresponding ones as target/query sequences is as follows:
| Tool/term | TPs/FPs/TNs/FNs | F-meas. | DB[s] | Align.[s] | |-----------|-----------------|---------|----------|---------------| | CRAST | 65/107/0/0 | 0.548 | 189.5[m] | 148.0 (34.60) | | LAST | 63/585/1/0 | 0.177 | 7.246 | 0.193 | | BLASTN | 63/1,834/445/0 | 0.064 | 1.646 | 1.152 | | BLAT | 40/141/0/0 | 0.361 | - | 4.893 |
The "align. time" of CRAST inside the parentheses is time except for the pre-processing. (The bzip2 decompression is time-consuming.)
The "TP" is map of any human one to any corresponding house mouse one; the "FP" is any human one to any of the others.
As a negative dataset, we made all the query ones di-nucleotide shuffled with UShuffle.
The "TN" is map of any shuffled query one to any of others than corresponding target ones; the "FN" is any shuffled query one to any of corresponding target ones.
The dependency in this project is the bzip2 program (for database file compression).
You can install it in case of Ubuntu as follows:
bash
$ sudo apt-get install bzip2
This project has been written by Rust, a systems programming language.
So first you need to install the Rust compiler (Rustc), Rust package manager (Cargo) and Rust standard library.
Please visit the Rust website to see more about it.
You can install them with 1 line as follows:
bash
$ curl https://sh.rustup.rs -sSf | sh
The above installation is done by Rustup, so you can easily switch the compiler to use.
Now you can install CRAST as follows:
bash
$ cargo install --git https://github.com/heartsh/crast
Check if it has been installed properly as follows:
bash
$ crast-db && crast
If you're interested in how much fast it is, run the benchmark as follows:
bash
$ git clone https://github.com/heartsh/crast && cd crast
$ tar xvf asts.tar.bz2
$ cargo test --release -- --nocapture
Copyright (c) 2016 Heartsh
Licensed under the MIT license.