https://github.com/enthought/vpsearch

Fast similarity search for genomic sequences via vantage-point trees
https://github.com/enthought/vpsearch

Last synced: 8 months ago
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Fast similarity search for genomic sequences via vantage-point trees

• Host: GitHub
• URL: https://github.com/enthought/vpsearch
• Owner: enthought
• License: other
• Created: 2019-07-29T20:14:42.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2023-08-22T01:30:02.000Z (almost 3 years ago)
• Last Synced: 2025-01-28T10:47:46.511Z (over 1 year ago)
• Language: Cython
• Homepage: https://vpsearch.readthedocs.io/en/latest/
• Size: 127 KB
• Stars: 4
• Watchers: 24
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGES.txt
  • Contributing: docs/contributing.rst
  • License: LICENSE
  • Code of conduct: docs/code_of_conduct.rst

Awesome Lists containing this project

README

          
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vpsearch - Fast Vantage-Point Tree Search for Sequence Databases

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[![PyPI version](https://badge.fury.io/py/vpsearch.svg)](https://badge.fury.io/py/vpsearch)

![Tests status](https://github.com/enthought/vpsearch/actions/workflows/run-tests.yaml/badge.svg?event=push)

[![DOI](https://joss.theoj.org/papers/10.21105/joss.04236/status.svg)](https://doi.org/10.21105/joss.04236)

This is a package for indexing and querying a sequence database for fast

nearest-neighbor search by means of [vantage point

trees](https://en.wikipedia.org/wiki/Vantage-point_tree). For reasonably large

databases, such as [RDP](https://rdp.cme.msu.edu/), 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](https://vpsearch.readthedocs.io/en/latest/).

## 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](LICENSE).