System and method for identification of MicroRNA target sites and corresponding targeting MicroRNA sequences

Abstract

A method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto is provided. For example, in one aspect of the invention, a method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto is comprised of the following steps. One or more patterns are generated by processing a collection of known mature microRNA sequences. The reverse complement of each generated patter is then computed. One or more attributes are then assigned to the reverse complement of the one or more generated patterns. The one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion are thereafter subselected. Each subselected pattern is then used to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.

1 . A method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto, the method comprising the steps of: 
 generating one or more patterns by processing a collection of known mature microRNA sequences;    generating a reverse complement of each generated pattern;    assigning one or more attributes to the reverse complement of the one or more generated patterns;    subselecting the one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion; and    using each subselected pattern to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.    
   
   
       2 . The method of  claim 1 , wherein the step of generating one or more patterns comprises using a pattern discovery algorithm.  
   
   
       3 . The method of  claim 2 , wherein the pattern discovery algorithm is the Teiresias pattern algorithm.  
   
   
       4 . The method of  claim 1 , wherein the step of assigning one or more attributes is carried out independently of and prior to the step of using the one or more patterns to analyze the nucleotide sequence.  
   
   
       5 . The method of  claim 1 , wherein the one or more attributes are quantitative.  
   
   
       6 . The method of  claim 5 , wherein at least one of the one or more attributes represents statistical significance.  
   
   
       7 . The method of  claim 5 , wherein at least one of the one or more attributes represents a length of the pattern.  
   
   
       8 . The method of  claim 5 , wherein the at least one of the one or more attributes represents a number of positions in the one or more patterns which are not occupied by wild cards.  
   
   
       9 . The method of  claim 1 , wherein a threshold value for each attribute is selected.  
   
   
       10 . The method of  claim 9 , wherein one or more patterns are discarded if the value of the one or more attributes of each pattern is below the selected threshold for the one or more attributes.  
   
   
       11 . The method of  claim 10 , wherein the steps of selecting a threshold value and discarding one or more patterns are repeated for all used attributes.  
   
   
       12 . The method of  claim 1 , wherein a set of counters is created for the nucleotide sequence.  
   
   
       13 . The method of  claim 12 , wherein the counters in the set of counters equal the number of nucleotides in the nucleotide sequence.  
   
   
       14 . The method of  claim 1 , wherein all patterns are examined to determine whether one or more patterns have an instance in the nucleotide sequence.  
   
   
       15 . The method of  claim 14 , wherein each pattern with an instance in the nucleotide sequence contributes to the counters at the corresponding positions of the nucleotide sequence.  
   
   
       16 . The method of  claim 15 , wherein only consecutive positions in the nucleotide sequences whose corresponding counter values exceed a threshold are considered.  
   
   
       17 . The method of  claim 16 , wherein one or more groups of consecutive positions is reported if the one or more groups of consecutive positions satisfy a minimum length criterion.  
   
   
       18 . The method of  claim 17 , wherein the one or more groups of consecutive positions are augmented by adding one or more flanking regions.  
   
   
       19 . The method of  claim 18 , wherein the one or more augmented groups span at most 36 positions.  
   
   
       20 . The method of  claim 19 , wherein the one or more augmented groups are reported.  
   
   
       21 . The method of  claim 20 , wherein the one or more reported groups are examined together with one or more microRNA sequences.  
   
   
       22 . The method of  claim 21 , wherein the one or more reported groups and the one or more microRNA sequence are hybridized into one or more complexes using one or more computational schemes.  
   
   
       23 . The method of  claim 22 , wherein at least one of the one or more computational schemes is an RNA secondary structure prediction method.  
   
   
       24 . The method of  claim 23 , wherein the prediction method is one included with software known as the Vienna Package.  
   
   
       25 . The method of  claim 23 , wherein the prediction method is a method called ‘mfold’.  
   
   
       26 . The method of  claim 22 , wherein the one or more predicted complexes are assigned one or more attributes.  
   
   
       27 . The method of  claim 26 , wherein at least one of the one or more attributes is free energy of the one or more formed complexes.  
   
   
       28 . The method of  claim 26 , wherein at least one of the one or more attributes is a number of matching pairs in the one or more formed complexes.  
   
   
       29 . The method of  claim 26 , wherein at least one of the one or more attributes is a number of bulges in the formed complex.  
   
   
       30 . The method of  claim 26 , wherein a threshold value is selected for each attribute.  
   
   
       31 . The method of  claim 26 , wherein one or more complexes are discarded if one or more attribute values does not exceed the selected threshold for the one or more attributes.  
   
   
       32 . The method of  claim 31 , wherein the steps of selecting a threshold value and discarding one or more patterns are repeated for all used attributes.  
   
   
       33 . The method of  claim 32 , wherein the nucleotide sequence and the one or more microRNA sequence forming the one or more complex are reported if the one or more complexes have not been discarded.  
   
   
       34 . A system for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto, comprising: 
 a memory that stores computer-readable code; and    a processor operatively coupled to the memory, the processor configured to implement the computer-readable code, the computer-readable code configured to:    generate one or more patterns by processing a collection of known mature microRNA sequences;    generate a reverse complement of each generated pattern;    assign one or more attributes to the reverse complement of the one or more generated patterns;    subselect the one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion; and    use each subselected pattern to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.    
   
   
       35 . An article of manufacture for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto, comprising: 
 a computer-readable medium having computer-readable code embodied thereon, the computer-readable code comprising: 
 a step to generate one or more patterns by processing a collection of known mature microRNA sequences;  
 a step to generate a reverse complement of each generated pattern;  
 a step to assign one or more attributes to the reverse complement of the one or more generated patterns;  
 a step to subselect the one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion; and  
 a step to use each subselected pattern to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.