Patent ID: 7565248

Claim:
A computer implemented method for determining an optimal reagent oligonucleotide sequence for use in a biochemical method for evaluating a target nucleic acid sequence having a target feature, the computer implemented method comprising using a computer programmed to execute each of the following steps: (a) receiving a set of exclusion values and/or ranking values specific to the biochemical method, (b) receiving sequence windows that are within 30 kb of a target feature or encompass the target feature for both the sense and antisense strands of the target nucleic acid sequence, wherein the sequence windows have a start and a stop position, (c) generating candidate reagent oligonucleotide sequences complementary to one or both of the sense and antisense strands of the target nucleic acid sequence within each sequence window by moving the sequence window one base at a time from the start position to the stop position, the reagent oligonucleotide sequences having a length less than or equal to the sequence window, (d) evaluating the candidate reagent oligonucleotide sequences against the exclusion and/or ranking parameters, wherein candidate oligonucleotide sequences that satisfy the exclusion and/or ranking parameters are retained, (e) selecting at least one retained candidate oligonucleotide sequence for use in the selected biochemical method as applied to the target nucleic acid sequence and displaying the retained sequence in a graphical user interface or storing the retained sequence on a computer readable medium.