https://github.com/audy/miniblast

The usual seed and extend search algorithm implemented in Ruby.
https://github.com/audy/miniblast

Last synced: about 18 hours ago
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The usual seed and extend search algorithm implemented in Ruby.

• Host: GitHub
• URL: https://github.com/audy/miniblast
• Owner: audy
• License: mit
• Created: 2011-05-25T19:21:19.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2015-04-28T03:21:33.000Z (over 9 years ago)
• Last Synced: 2024-04-14T19:08:47.433Z (6 months ago)
• Language: Ruby
• Homepage:
• Size: 110 KB
• Stars: 1
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md
  • License: license.md

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README

        
# miniblast

The usual seed and extend search algorithm implemented in Ruby.

    miniblast database.fasta query.fasta [kmer_length]

While other men tune their Z28s, I hack away at miniblast.

## What it do?

- Finds you a string that has the largest matching substring to your query string.

- Uses all your cores (and memory).

- Is fast.

	

## What it don't?

- Provide any information about the quality of the match given 'cause who needs that?

## Requirements

- Ruby 1.8.7 or 1.9.2 (if you want to go _faaast!_)

- [Parallel](https://github.com/grosser/parallel)

- [snappy-ruby](https://github.com/delta407/snappy-ruby)

- [ruby-trie](https://github.com/jaronson/ruby-trie)