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

1. Pick the correct binary for your machine in the release
2. Place it in a nice location on your machine
3. If you are using a unix-based operating system (linux or mac) do not forget to chmod +x <binary>
4. Open a terminal and use the tool
5. 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

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

From source

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

Quick usage overview

1. 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).
2. 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.
3. 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
4. List IMGT genes align --imgt or align --specific-gene <GENE>.

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

Example usage

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