Methods for selecting nucleic acid probes
AssigneeAffymetrix, Inc.
InventorEarl Hubbell
Life of this patent
Estimating the term…
Abstract
Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, dynamic programming is employed to select a set of k probes from n probes so that the selected probes have a maximum aggregate adjusted quality score.
Claims27
A computer implemented method for selecting nucleic acid probes comprising:
- inputting quality scores and locations for a plurality (n) of candidate probes;
- selecting k number of probes from the n number of candidate probes, wherein the selected probes have a maximum aggregate adjusted quality score;
- wherein the adjusted quality score is based upon the quality score and a penalty for the overlapping of the selected probes;
- and
- outputting the selected probes.
A system for selecting nucleic acid probes comprising:
- a processor;
- and
- a memory coupled with the processor, the memory storing a plurality of machine instructions that cause the processor to perform logical steps, wherein the logical steps include:
- inputting quality scores and locations for a plurality (n) of candidate probes;
- selecting k number of probes from the n number of candidate probes, wherein the selected probes have a maximum aggregate adjusted quality score;
- wherein the adjusted quality score is based upon the quality score and a penalty for the overlapping of the selected probes;
- and
- outputting the selected probes.
A computer readable medium having computer executable instructions for performing a method comprising:
- inputting quality scores and locations for a plurality (n) of candidate probes;
- selecting k number of probes from the n number of candidate probes, wherein the selected probes have a maximum aggregate adjusted quality score;
- wherein the adjusted quality score is based upon the quality score and a penalty for the overlapping of the selected probes;
- and
- outputting the selected probes.
A computer implemented method for selecting nucleic acid probes comprising:
- inputting quality scores and locations for a plurality (n) of candidate probes;
- selecting k number of probes from the n number of candidate probes, wherein the selected probes have a maximum aggregate adjusted quality score;
- wherein the adjusted quality score is based upon the quality score and a penalty for the overlapping of the selected probes;
- and
- outputting the selected probes, wherein the outputting of the selected probe sequences is to a file.
A system for selecting nucleic acid probes comprising:
- a processor;
- and
- a memory coupled with the processor, the memory storing a plurality of machine instructions that cause the processor to perform logical steps, wherein the logical steps include:
- inputting quality scores and locations for a plurality (n) of candidate probes;
- selecting k number of probes from the n number of candidate probes, wherein the selected probes have a maximum aggregate adjusted quality score;
- wherein the adjusted quality score is based upon the quality score and a penalty for the overlapping of the selected probes;
- and
- outputting the selected probes, wherein the outputting of the selected probe sequences is to a file.
A computer readable medium having computer executable instructions for performing a method comprising:
- inputting quality scores and locations for a plurality (n) of candidate probes;
- selecting k number of probes from the n number of candidate probes, wherein the selected probes have a maximum aggregate adjusted quality score;
- wherein the adjusted quality score is based upon the quality score and a penalty for the overlapping of the selected probes;
- and
- outputting the selected probes, wherein the outputting of the selected probe sequences is to a file.
Dependencies are inferred from the claim text.