Systems and methods for rational selection of context sequences and sequence templates

Abstract

Provided are systems and methods for rational selection of context sequences and sequence templates including a computer implemented method for obtaining a repository of attributes sets where the attributes sets are statistically associated with a sequence template representing two or more context sequences.

1 - 16 . (canceled) 
     
     
         17 . A computer readable non-transitory memory comprising a random-access memory (RAM) and a secondary storage, the computer readable memory storing a distance matrix data structure configured to store data items comprising references pointing at two objects and a real number being a measured distance calculated by a distance formula,
 wherein the distance matrix data structure is implemented with a multiple-tree-array, and   wherein the multiple tree array comprises a root node and a plurality of heaps, such that at least one of the heaps is stored in the RAM as an active heap, and at least one of the heaps is stored in the secondary storage as a passive heap.   
     
     
         18 . The computer readable non-transitory memory of  claim 17 , wherein the multiple-tree-array is configured to replace or switch at least one of the active heaps with at least one passive heap in order to ensure the dominance of a heap invariant when a Delete( ) procedure erased a global minimum or maximum from the multiple-tree-array,
 wherein the heap invariant according to which the top or bottom data item in the multiple-tree-array is a data item having the minimal measured distance in the multiple-tree-array.   
     
     
         19 . The computer readable non-transitory memory of  claim 17 , wherein said heaps are min heaps. 
     
     
         20 . The computer readable non-transitory memory of  claim 17 , wherein said heaps are max heaps. 
     
     
         21 . The computer readable non-transitory memory of  claim 17 , wherein the plurality of heaps represents a plurality of tree topologies, wherein the plurality of tree topologies is configured to be managed through a common interface. 
     
     
         22 . The computer readable non-transitory memory of  claim 17 , wherein the data items which are stored comprise references pointing at two objects and a real number, wherein the data items represent a cluster of context sequences and the real number measures the distance between the context sequences, wherein the cluster of context sequences comprises a set of gene unique identifiers which are operably linked by the context sequences within the cluster. 
     
     
         23 . A computer implemented method for obtaining a computer readable non-transitory memory comprising attributes sets stored therein, wherein attributes sets are statistically associated with a sequence template representing two or more context sequences, comprising:
 (a) obtaining a dataset of context sequences;   (b) transforming each context sequence to a sequence template, thereby obtaining a dataset of sequence templates;   (c) clustering said dataset of sequence templates into a plurality of clusters according to a distance formula, wherein at least one cluster is statistically associated with at least one attributes set; and   (d) inserting into said computer readable non-transitory memory each of said clusters and said attributes set which is statistically associated with said each of said clusters.   
     
     
         24 . The computer implemented of  claim 23 , wherein said dataset of context sequences of step (a) is further subjected to multiple sequence alignment. 
     
     
         25 . A computer readable non-transitory memory obtained by the computer implemented method of  claim 23 , said computer readable non-transitory memory comprising a random-access memory (RAM) and a secondary storage. 
     
     
         26 . A method of preparing a polynucleotide construct, comprising:
 (a) identifying a sequence template as statistically associated with an attributes set of interest according to the method of  claim 23 ;   (b) preparing a polynucleotide construct having at least one portion operably linked to a context sequence; wherein said context sequence is characterized as having either 80%-85%, 85%-90%, or 90%-100% homology with said sequence template.   
     
     
         27 . The method of  claim 26 , wherein the preparing comprises synthesizing said context sequence. 
     
     
         28 . The method of  claim 26 , wherein the preparing comprises constructing an expression vector comprising said context sequence. 
     
     
         29 . The method of  claim 26 , wherein the preparing comprises constructing a probe comprising said context sequence.