Computer-aided visualization and analysis system for sequence evaluation

Abstract

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

1 - 44 . (canceled)  
     
     
         45 . A computer implemented method of displaying sequences of bases, the method comprising: 
 displaying at least one reference sequence on a display device;    evaluating hybridization between at least one sample sequence and nucleic acid probes in order to call bases of said at least one sample sequence;    separately displaying said at least one sample sequence on said display device, wherein said displayed reference and sample sequences are displayed so that bases at a same position in said displayed reference and sample sequences are aligned on said display device;    receiving user input to select a plurality of displayed sequences for comparison by the computer system;    comparing said selected sequences; and    indicating on said display device bases that differ between or among the selected sequences at the same position including indicating bases in a selected sample sequence that differ from bases at corresponding positions in a selected reference sequence.    
     
     
         46 . The method of  claim 45 , further comprising indicating on said display device said selected sequences.  
     
     
         47 . The method of  claim 45 , further comprising displaying a common symbol on said display device next to said selected sequences.  
     
     
         48 . The method of  claim 45 , wherein said common symbol is a number.  
     
     
         49 . The method of  claim 45 , wherein said at least one reference sequence and said at least one sample sequence are monomer strands of DNA or RNA.  
     
     
         50 . The method of  claim 45 , wherein said bases are A, C, G, or T(U).  
     
     
         51 . The method of  claim 45 , wherein said at least one reference sequence includes a chip wild-type sequence.  
     
     
         52 . The method of  claim 51 , wherein said chip wild-type sequence is displayed as the first sequence.  
     
     
         53 . The method of  claim 51 , further comprising displaying a label to identify said chip wild-type sequence.  
     
     
         54 . The method of  claim 53 , wherein said label is a capital C.  
     
     
         55 . The method of  claim 45 , further comprising: 
 displaying a name associated with each of said at least one reference sequence; and    displaying a name associated with each of said at least one sample sequence.    
     
     
         56 . A computer program product that displays sequences of bases, comprising: 
 computer code that displays at least one reference sequence on a display device;    computer code that evaluates hybridization between at least one sample sequence and nucleic acid probes in order call bases of said at least one sample sequence;    computer code that separately displays said at least one sample sequence on said display device, wherein said displayed reference and sample sequences are displayed so that bases at a same position in said displayed reference and sample sequences are aligned on said display device;    computer code that receives user input to select a plurality of displayed sequences for comparison by a computer system;    computer code that compares said selected sequences;    computer code that indicates on said display device bases that differ between or among the selected sequences at corresponding positions including indicating bases in a selected sample sequence that differ from bases at corresponding positions in a selected reference sequence; and    a computer readable medium that stores said computer codes.    
     
     
         57 . The computer program product of  claim 56 , further comprising computer code that indicates on said display device said selected sequences.  
     
     
         58 . The computer program product of  claim 56 , further comprising computer code that displays a common symbol on said display device next to said selected sequences.  
     
     
         59 . The computer program product of  claim 58 , wherein said common symbol is a number.  
     
     
         60 . The computer program product of  claim 56 , wherein said at least one reference sequence and said at least one sample sequence are monomer strands of DNA or RNA.  
     
     
         61 . The computer program product of  claim 56 , wherein said bases are A, C, G, or T(U).  
     
     
         62 . The computer program product of  claim 56 , wherein said at least one reference sequence includes a chip wild-type sequence.  
     
     
         63 . The computer program product of  claim 62 , wherein said chip wild-type sequence is displayed as the first sequence.  
     
     
         64 . The computer program product of  claim 62 , further comprising computer code that displays a label to identify said chip wild-type sequence.  
     
     
         65 . The computer program product of  claim 64 , wherein said label is a capital C.  
     
     
         66 . The computer program product of  claim 56 , further comprising: 
 computer code that displays a name associated with each of said at least one reference sequence; and    computer code that displays a name associated with each of said at least one sample sequence.