Method of designing probe set, microarray having substrate on which probe designed by the method is immobilized, and computer readable medium on which program for executing the method is recorded

• US 20060058967A1
• Filed: 09/14/2005
• Published: 03/16/2006
• Est. Priority Date: 09/14/2004
• Status: Active Grant

• Current Assignee: Samsung Electronics Co. Ltd.
• Original Assignee: Samsung Electronics Co. Ltd.
• Inventors: Kwon, Tae-joon
• Granted Patent: US 7,657,381 B2
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence

Abstract

A method of designing a probe set for identifying a target sequence from a plurality of target sequence groups by a hybridization reaction is provided. The method includes: (a) selecting a first target sequence group including a plurality of target sequences; (b) selecting oligonucleotides specifically binding to the target sequences from the first target sequence group as a probe; (c) selecting one or more target sequences having no specifically binding probe from the first target sequence group as a second target sequence group; (d) selecting oligonucleotides specifically binding to the target sequences from the second target sequence group as a probe, wherein the operations (c) and (d) are repeated until a target sequence having no specifically binding probe is absent in the second target sequence group.

Claims

1. A method of designing a probe set for identifying a target sequence from a plurality of target sequence groups by hybridization, comprising:

(a) selecting a first target sequence group including a plurality of target sequences;

(b) selecting oligonucleotides specifically binding to the target sequences from the first target sequence group as a probe;

(c) selecting one or more target sequences having no specifically binding probe from the first target sequence group as a second target sequence group;

(d) selecting oligonucleotides specifically binding to the target sequences from the second target sequence group as a probe,

wherein the operations (c) and (d) are repeated until a target sequence having no specifically binding probe is absent in the second target sequence group.

2. The method according to claim 1, wherein when it is impossible to additionally select a specific probe because of high sequence homology among the sequences in the second target sequence group, a sequence present in common in the second target sequence group, but not present in other target sequences of the first target sequence group or the complementary sequence thereof is selected as a probe.

3. A polynucleotide microarray having a substrate on which the probe set designed by the method according to claim 1 is immobilized.

4. A computer readable medium on which a program for executing the method according to claim 1 is recorded.