Installing the `align` executable

Assuming you have Rust/Cargo installed, run this command in a terminal:

cargo install align-cli

It will make the align command available in your PATH if you've allowed the PATH to be modified when installing Rust. cargo uninstall align-cli uninstalls.

Back to the crate overview.

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 <binary>
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 <FILE.fasta>.
- 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 <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 <sequence>, this shows many basic properties (like mass) and generates isobaric sequences to this sequence.
- Use --fixed <MODIFICATIONS> and --variable <MODIFICATIONS> to fine tune the generated isobaric sequences.
Get information about a single modification align --modification <MODIFICATION>.
- Use a full name to list its properties eg --modification Oxidation
- Use a formula to find all modifications with that formula eg --modification Formula:O
- Use a mass to find all modifications with that mass eg --modification +15.995
List IMGT genes align --imgt or align --specific-gene <GENE>.

For all additional options and more description use align --help.

Example usage

example of calling with pairwise alignment example of calling with complex alignment example of calling with single sequence example of calling with named modification example of calling with mass modification

Here are the used commands for reference

> align AKTNLSHLGYGMDV AKEGGLHSIGYGMDV
> align AKTNLNHLGY BHJGYGMDV --local --context
> align GAI
> align --modification 23 --tolerance 0.5da
> align -m Oxidation
> align --species human --domain -N 1 -n 70 EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Installing the align executable

Installing the `align` executable