Patent Document ID: 9779205
Application ID: 13764894
Patent Flag: 1

Claim One:
1. A computer implemented method for identifying a sequence template as statistically associated with plant functional annotations of interest, the method implemented on a computer comprising a processor, and computer readable memory comprising RAM and secondary storage, the method comprising: (a) obtaining, using the processor, a first plant functional annotation set comprising at least one plant functional annotation from a user; (b) obtaining, using the processor, a data repository comprising polynucleotide plant mRNA sequences and storing the data repository in the computer readable memory; and (c) for each mRNA sequence, identifying, using the processor, the translation initiation codon and a corresponding context sequence comprising a stretch of nucleotides preceding the translation initiation codon; (d) transforming, using the processor, each of the context sequences into a sequence template; (e) allocating, in the computer readable memory, a multiple-tree-array data structure, the multiple-tree-array consisting of a root node and a plurality of heaps, at least one of the heaps being stored in the RAM and at least one of the heaps being stored in the secondary storage; (f) inserting, using the processor, data items into the multiple-tree-array, the data items comprising two sequence templates and a distance between the sequence templates; (g) clustering, using the processor, the sequence templates, wherein the clustering comprises retrieving data items from the multiple-tree-array, storing data items in the multiple-tree-array, and merging the sequence templates in a cluster into a common sequence template that represents all of the templates within the cluster; (h) selecting, using the processor, a cluster; (i) obtaining, using the processor, a list of plant functional annotations that are statistically overrepresented within said cluster; and (j) storing the sequence template and the functional annotations of said cluster in the computer readable memory.