Biological sequence variant characterization

A method for determining a signature from biological sequence data, comprising:

• extracting short fixed length sub-sequences, defined as reference sub-sequences, from a collection of reference sequences, and constructing an index showing which short fixed length reference sub-sequence occurs in which reference sequences;
• extracting short fixed length sub-sequences, the same length as the reference sub-sequences and defined as source sub-sequences, from a collection of source sequences derived from a sample for which the signature is to be determined, and compiling the short fixed length source sub-sequences to determine the frequency of each within the collection;
• and
• using the presence or absence of source sub-sequences in combination with the index to infer the presence or absence of reference sequences from the reference collection;
• wherein one or more of the above steps are performed in accordance with a processor and a memory.