Biological sequence tandem repeat characterization

An article of manufacture comprising a computer readable storage medium for storing computer readable program code which, when executed, causes a computer node to perform the steps of:

• extracting short fixed length source sub-sequences from a collection of source sequences derived from a sample for which the biological signature is to be determined;
• compiling the extracted short fixed length source sub-sequences to determine the frequency of each within the collection;
• using overlaps between the short fixed length source sub-sequences to find a chain of overlaps from one or more sub-sequences equivalent to a pre-flanking reference marker sequence to one or more sub-sequences equivalent to a post-flanking reference marker sequence, the reference marker sequences flanking a region containing a repetitive sequence region;
• and
• in response to the chain containing multiple instances of the one or more short fixed length source sub-sequences, thereby defining a cycle, examining the sequences from the collection derived from the sample to find one or more sequences that span the cycle, and at least one of:
• (i) using the lengths of the spanning sequences to determine the length of the cycle and;
• (ii) counting the number of repeat motif copies within each spanning sequence;
• wherein one or more of the above steps are performed in accordance with a processor and a memory.

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

• a memory;
• and
• a processor operatively coupled to the memory and configured to:
• extract short fixed length source sub-sequences from a collection of source sequences derived from a sample for which the biological signature is to be determined;
• compile the extracted short fixed length source sub-sequences to determine the frequency of each within the collection;
• use overlaps between the short fixed length source sub-sequences to find a chain of overlaps from one or more sub-sequences equivalent to a pre-flanking reference marker sequence to one or more sub-sequences equivalent to a post-flanking reference marker sequence, the reference marker sequences flanking a region containing a repetitive sequence region;
• and
• in response to the chain containing multiple instances of the one or more short fixed length source sub-sequences, thereby defining a cycle, examine the sequences from the collection derived from the sample to find one or more sequences that span the cycle, and at least one of:
• (i) use the lengths of the spanning sequences to determine the length of the cycle and;
• (ii) count the number of repeat motif copies within each spanning sequence.