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VPsearch

VPsearch: fast exact sequence similarity search for genomic sequences - Published in JOSS (2022)

https://github.com/enthought/vpsearch

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Biology Life Sciences - 40% confidence
Last synced: 4 months ago · JSON representation

Repository

Fast similarity search for genomic sequences via vantage-point trees

Basic Info
Statistics
  • Stars: 4
  • Watchers: 23
  • Forks: 1
  • Open Issues: 1
  • Releases: 1
Created over 6 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.md

vpsearch - Fast Vantage-Point Tree Search for Sequence Databases

PyPI version Tests status DOI

This is a package for indexing and querying a sequence database for fast nearest-neighbor search by means of vantage point trees. For reasonably large databases, such as RDP, this results in sequence lookups that are typically 5-10 times faster than other alignment-based lookup methods.

Vantage-point tree search uses global-to-global alignment to compare sequences, rather than seed-and-extend approximative methods as used for example by BLAST.

Installation and usage

VPsearch can be installed and updated through pip: console pip install -U vpsearch

This will install a standalone command-line utility vpsearch into your environment, which can be used to build and query a sequence database. For more information on how to do so, see the documentation.

Citing vpsearch

If you use vpsearch, please cite our paper:

  • Joris Vankerschaver, Steven J. Kern, Robert Kern. VPsearch: fast exact sequence similarity search for genomic sequences. Journal of Open Source Software, 7(78), 4236, 2002. https://doi.org/10.21105/joss.04236

License

This package is licensed under the 3-clause BSD license.

Owner

  • Name: Enthought, Inc.
  • Login: enthought
  • Kind: organization
  • Location: Austin, TX

JOSS Publication

VPsearch: fast exact sequence similarity search for genomic sequences
Published
October 08, 2022
DOI
Volume 7, Issue 78, Page 4236
Authors
Joris Vankerschaver ORCID
Center for Biosystems and Biotech Data Analysis, Ghent University Global Campus, Republic of Korea, Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium
Steven J. Kern ORCID
Enthought Inc., 200 W Cesar Chavez, Austin, TX 78701, United States
Robert Kern
Enthought Inc., 200 W Cesar Chavez, Austin, TX 78701, United States
Editor
Lorena Pantano ORCID
Tags
python genomics bioinformatics
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GitHub Events

Total
Last Year

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 91
  • Total Committers: 7
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.407
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Joris Vankerschaver j****r@g****m 54
Joris Vankerschaver j****r@e****m 25
Peter Zahemszky p****y@e****m 6
Robert Kern r****n@e****m 3
atlantis-gh-enthought 4****t 1
Mark Dickinson m****n@e****m 1
KERNS11 s****n@e****m 1
Committer Domains (Top 20 + Academic)
enthought.com: 5

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 12
  • Total pull requests: 30
  • Average time to close issues: 2 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 1.92
  • Average comments per pull request: 1.63
  • Merged pull requests: 30
  • 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
View more stats
Top Authors
Issue Authors
  • jvkersch (8)
  • sdhutchins (3)
  • tamarahadz (1)
Pull Request Authors
  • jvkersch (28)
  • mdickinson (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 95 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 3
  • Total maintainers: 2
pypi.org: vpsearch

Global-Global genetic database search.

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 95 Last month
Rankings
Dependent packages count: 10.0%
Average: 20.5%
Dependent repos count: 21.7%
Forks count: 22.6%
Stargazers count: 23.0%
Downloads: 25.1%
Maintainers (2)
enthought jvkersch
Last synced: 4 months ago

Dependencies

.github/workflows/build-wheels.yml actions
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  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
.github/workflows/run-tests.yaml actions
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Dockerfile docker
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requirements.txt pypi
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setup.py pypi
  • Pin *
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  • https *
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  • parasail ==1.3.3
data/environment.yml pypi
pyproject.toml pypi