Use this command to install AlignCli:

winget install --id=Snijderlab.AlignCli -e

A command line interface for easily aligning sequences.

AlignCli is a command-line interface tool designed for aligning protein sequences with support for both normal and mass-based alignment methods. It offers researchers a versatile solution for sequence analysis.

Key Features:

Perform pairwise alignments of peptides using various modes, including global and local alignment options.
Compare single peptides against databases or specific genes within the IMGT database.
Generate isobaric sequences to explore potential modifications and obtain detailed information on chemical modifications.
Access features to list IMGT genes and retrieve information about specific genes.

Audience & Benefit: Ideal for researchers in proteomics, mass spectrometry, and bioinformatics who require efficient sequence analysis. AlignCli enhances the ability to study protein interactions, identify post-translational modifications, and conduct comparative genomics by providing precise alignment tools and comprehensive data exploration capabilities. Install via winget on Windows for easy setup.

README

Align-cli

A tool to help your manual mass spec inspection workflow. With alignments, isobaric sequences, and other mass spec information.

Installing

Using winget

On windows use winget install --id Snijderlab.AlignCli.

From binary

Pick the correct binary for your machine in the release
Place it in a nice location on your machine
If you are using a unix-based operating system (linux or mac) do not forget to chmod +x
Open a terminal and use the tool
If you want you can add the location of the binary to your path, this makes it so that you can use it across your whole machine

More elaborate instructions for Windows (installing another program)

With cargo

First install Rust.
Install the tool using cargo (part of Rust) cargo install align-cli

From source

First install Rust.
Clone the repository.
Build with cargo cargo build --release
Or, if you want to install cargo install --path ..

Quick usage overview

Pairwise alignment
- Align two sequences align <a> <b>, this shows the best alignment for these two sequences.
- Align a single peptide to a database align <a> --file .
- Align a single peptide to the IMGT database align <a> --imgt.
- Align a single peptide to the V-J-C domains in the IMGT database align <a> --domain.
- Align a single peptide to a specific gene in IMGT database align <a> --specific-gene .
- For any of these you can control if the peptides have to allign fully (--global), if you want to see the best possible subsequence alignment (--local), or a more elaborate mode (see --help and --type).
Get information about a single sequence align , this shows many basic properties (like mass) and generates isobaric sequences to this sequence.
- Use --fixed and --variable to fine tune the generated isobaric sequences.

AlignCli Snijderlab