Abstract: We disclose a combinatorial, hierarchical process that uses “process-patterns” in one preferred embodiment to identify, classify, and compare substrings within strings; and in another preferred embodiment to identify, classify, compare, generate, and separate fragments derived from one or more physical samples of polynucleotides. These substrings (and their physical polynucleotide counterparts) are called “partition” fragments, and the process-pattern-defined derivatives that some, but not all, “partition” fragments may yield are called “structured query fragments” (SQFs).