crast 1.0.0

CRAST, Context RNA Alignment Search Tool
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54

# CRAST, Context RNA Alignment Search Tool
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.

# Dependencies
The dependency in this project is [the bzip2 program](http://bzip.org/) (for database file compression).
You can install it in case of Ubuntu as follows:
```bash
$ sudo apt-get install bzip2
```

# Installation
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](https://www.rust-lang.org) 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](https://github.com/rust-lang-nursery/rustup.rs), 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
```

# Author
[Heartsh](https://github.com/heartsh)

# License
Copyright (c) 2016 Heartsh  
Licensed under [the MIT license](http://opensource.org/licenses/MIT).