ReAlign-Star: an optimized realignment method for multiple sequence alignment, targeting star algorithm tools

ReAlign-Star is a tool written in C++17 for realigning the multiple nucleic acid sequence alignment (star algorithm tools). It runs on Linux.

🔨Installation and Usage

1 Linux/WSL(Windows Subsystem for Linux ) - from the source code

1.Download and Compile the source code. (Make sure your version of gcc >= 9.4.0)

#1 Download
git clone https://github.com/malabz/ReAlign-Star.git

#2 Open the folder
cd ReAlign-Star

#3 Compile
make

#4 Test ReAlign-Star
./realign_star -h

2 Usage

Usage: ./realign_star -i <input_file> [-o <output_file>] [-w <window_size>] [-l <length>] [-m <msa>]

Options:
  -i <input_file>    (required) Path to the input file containing sequence data.
  -o <output_file>   (optional) Path to the output file for storing results. Default is 'realign_star_result.fasta'.
  -w <window_size>   (optional) Window size for sequence processing. Default is 10.
  -l <length>        (optional) Target length for sequence segments. Default is 5.
  -m <msa>           (optional) MSA tool to use, options are 'halign3', 'mafft', or 'muscle3'. Default is 'mafft'.

Examples:
  ./realign_star -i data.fasta -o results.fasta -w 20 -l 10 -m halign3
  ./realign_star -i data.fasta -m muscle3

Note:
  - The '-i' option is required.
  - The '-m' option only supports 'halign3', 'mafft', and 'muscle3'.
  - If '-w' or '-l' are not provided, default values of 10 and 5 will be used respectively.

🔬Test dataset and the use case

1. Information about the test dataset

Dataset	Sequences Num	Repeats Num	Avg Length	Similarity
23S rRNA	500	1	about 3120bp	The average similarity is about 92%
SARS-CoV-2 genome	156	1	about 29000bp	The average similarity is about 99%
SARS-CoV-2 genome	24310	1	about 29000bp	The average similarity is about 99%
16S-like rRNA	100	9	about 1550bp	14 sets of data with different similarities (99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 85%, 80%, 75%, 70%)
mt-like genome	100	9	about 16000bp	14 sets of data with different similarities (99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 85%, 80%, 75%, 70%)
SARS-CoV-2-like genome	100	9	about 29000bp	14 sets of data with different similarities (99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 85%, 80%, 75%, 70%)
CIPRES-128	255	9	about 1550bp	The average similarity is about 80%
CIPRES-256	511	9	about 1550bp	The average similarity is about 80%
CIPRES-512	1023	9	about 1550bp	The average similarity is about 80%
CIPRES-1024	2047	9	about 1550bp	The average similarity is about 80%
CIPRES-2048	4095	9	about 1550bp	The average similarity is about 80%
CIPRES-4096	8191	9	about 1550bp	The average similarity is about 80%

2. The use case

# Download data
wget http://lab.malab.cn/soft/ReAlign-Star/data/23s_rrna.tar.gz

# Unzip data
tar -zxvf 23s_rrna.tar.gz

# Run ReAlign-Star
./realign_star -i 23S_rRNA/halign3/23s_rRNA_halign3.fasta -o 23s_rrna_realign_star.fasta

📍Reminder

1. Currently ReAlign-Star is ONLY available for DNA/RNA.
2. Please ensure that the sequence ID entered into ReAlign-Star is unique.
3. HAlign3, MAFFT, MUSCLE3 installation is required for the utilization of ReAlign-Star.

🖥️Environment

System	GCC version
Linux	GCC 9.4.0
WSL	GCC 9.4.0

🔖Citation

👋Contacts

The software tools are developed and maintained by 🧑‍🏫ZOU's lab.

If you find any bug, welcome to contact us on the issues page or email us at 👉📩.

More tools and infomation can visit our github.