Computer system for designing oligonucleotides used in biochemical methods
AssigneeCeladon Laboratories, Inc.
InventorRaymond J Peterson
Life of this patent
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Abstract
A method for determining one or a set of optimal reagent oligonucleotide sequences used in a biochemical method for evaluating a target nucleic acid sequence having a target feature by defining a set of exclusion values or ranking values specific to the biochemical method, generating candidate reagent oligonucleotide sequences, evaluating the candidate reagent oligonucleotide sequences against the exclusion or ranking parameters, selecting at least one optimal reagent oligonucleotide sequence for the selected biochemical method as applied to the target nucleic acid sequence.
Claims34
A 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 method comprising the steps of:
- defining a set of exclusion values and/or ranking values specific to the biochemical method,
- defining a sequence window adjacent to the target feature,
- generating candidate reagent oligonucleotide sequences complementary to one or both of the sense and antisense strands of the target nucleic acid sequence within the sequence window, the reagent oligonucleotide sequences having a length less than or equal to the sequence window,
- evaluating the candidate reagent oligonucleotide sequences against the exclusion and/or ranking parameters, selecting at least one optimal reagent oligonucleotide sequence for the
- selected biochemical method as applied to the target nucleic acid sequence.
A computer system comprising:
- a database storing a plurality of target nucleic acid sequences having at least one target feature;
- a graphical user interface including:
- means for selecting a said target nucleic acid sequence from said database;
- means for selecting a biochemical method for evaluating the selected target nucleic acid sequence and
- means for displaying reagent oligonucleotide sequences that satisfy the exclusion and ranking parameters of said biochemical method;
- and
- a computer-readable data storage medium comprising program code means for defining a set of exclusion values and/or ranking values specific to the biochemical method, defining a sequence window adjacent to the target feature, generating candidate reagent oligonucleotide sequences complementary to one or both of the sense and antisense strands of the target nucleic acid sequence within the sequence window, the reagent oligonucleotide sequences having a length less than or equal to the sequence window, evaluating the candidate reagent oligonucleotide sequences against the exclusion and/or ranking parameters, selecting at least one optimal reagent oligonucleotide sequence for the selected biochemical method as applied to the target nucleic acid sequence.
Dependencies are inferred from the claim text.