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align-cli

A CLI for pairwise alignment of sequences, using both normal and mass based alignment.

https://github.com/snijderlab/align-cli

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
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  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary

Keywords

alignment mass-spectrometry protein rust
Last synced: 6 months ago · JSON representation ·

Repository

A CLI for pairwise alignment of sequences, using both normal and mass based alignment.

Basic Info
  • Host: GitHub
  • Owner: snijderlab
  • License: apache-2.0
  • Language: Rust
  • Default Branch: main
  • Homepage:
  • Size: 840 KB
Statistics
  • Stars: 13
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 11
Topics
alignment mass-spectrometry protein rust
Created over 2 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

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

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 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 ```

Owner

  • Name: snijderlab
  • Login: snijderlab
  • Kind: organization
  • Location: Netherlands

Research lab under @joostsnijder at the @UtrechtUniversity.

Citation (CITATION.cff) 

title: Align Command Line Interface (align-cli)
version: 0.4.0
abstract: A command line interface for pairwise alignment of sequences using mass-based alignment.
authors:
  - affiliation: Utrecht University
    family-names: Schulte
    given-names: Douwe
    orcid: https://orcid.org/0000-0003-0594-0993
  - affiliation: Utrecht University
    family-names: Snijder
    given-names: Joost
    orcid: https://orcid.org/0000-0002-9310-8226
cff-version: 1.2.0
identifiers:
  - description: Algorithm paper
    type: doi
    value: 10.1021/acs.jproteome.4c00188
  - description: Algorithm paper (preprint)
    type: url
    value: https://www.biorxiv.org/content/10.1101/2024.02.20.581155v1
  - description: Repository
    type: url
    value: https://github.com/snijderlab/align-cli
keywords:
  - sequencing
  - antibody
  - mass-spectrometry
  - de novo
license: MIT OR Apache-2.0
message: If you use this software, please cite it using these metadata.
repository-code: https://github.com/snijderlab/stitch

GitHub Events

Total
  • Release event: 1
  • Watch event: 5
  • Delete event: 1
  • Push event: 13
  • Create event: 2
Last Year
  • Release event: 1
  • Watch event: 5
  • Delete event: 1
  • Push event: 13
  • Create event: 2

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 118
  • Total Committers: 1
  • Avg Commits per committer: 118.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 22
  • Committers: 1
  • Avg Commits per committer: 22.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Douwe Schulte d****e@u****l 118
Committer Domains (Top 20 + Academic)
uu.nl: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Packages

  • Total packages: 1
  • Total downloads:
    • cargo 11,501 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 10
  • Total maintainers: 1
crates.io: align-cli

A command line interface for easily aligning sequences.

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 11,501 Total
Rankings
Dependent repos count: 28.4%
Dependent packages count: 33.1%
Average: 53.6%
Downloads: 99.3%
Maintainers (1)
douweschulte
Last synced: 6 months ago

Dependencies

.github/workflows/rust.yml actions
  • actions/checkout v4 composite
  • actions/upload-artifact v4 composite
  • dtolnay/rust-toolchain stable composite
  • softprops/action-gh-release v1 composite
Cargo.lock cargo
  • 116 dependencies
Cargo.toml cargo