audy / miniblast

The usual seed and extend search algorithm implemented in Ruby.

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
• snappy-ruby
• ruby-trie