Sequence Alignment Tool 🧬

A command-line tool for comparing protein sequences with high performance and flexibility.

Principle

The tool performs pairwise sequence alignments using either BLOSUM62 or identity scoring. It supports streaming output and optional pre-filtering based on k-mer matches to improve performance when dealing with large sequence sets.

Basic Usage

./aligner <input> [OPTIONS]

Arguments

Argument	Description
<input>	Path to your input JSON file containing the sequences

Options

Option	Description
-o, --output <FILE>	Specify output file path (tab-separated format)
-f, --fraction <FLOAT>	Set pre-filtering fraction using k-mer matches (0.0-1.0)
-m, --min-matches <INT>	Set minimum number of k-mer matches required for alignment (default: 0)
-s, --scoring <TYPE>	Choose scoring type: blosum62 or identity (default: identity)
-t, --threads <INT>	Set number of threads for parallel processing (default: 1)
-h, --help	Display help information
-V, --version	Show version information

Input Format

Your input file should be a JSON file structured as follows:

{
  "Q6A0I3": "MAVMT...",
  "ADV92528.1": "MANPY..."
}

Output Format

The tool generates a tab-separated output with the following columns:

query_id subject_id score seq1_len seq2_len
Q6A0I3 ADV92528.1 ... ... ...

Example Usage

./aligner input.json -o output.tsv -f 0.5 -s blosum62

This will:

• Read sequences from input.json
• Use BLOSUM62 scoring matrix
• Apply 50% k-mer pre-filtering
• Save results to output.tsv