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 7,657,381 B2
• Filed: 09/14/2005
• Issued: 02/02/2010
• Est. Priority Date: 09/14/2004
• Status: Expired due to Fees

• Current Assignee: Samsung Electronics Co. Ltd.
• Original Assignee: Samsung Electronics Co. Ltd.
• Inventors: Kwon, Tae-joon
• Primary Examiner(s): Zeman; Mary K
• Application Number:
  US11/226,082
• Publication Number:
  US 20060058967A1
• Time in Patent Office: 1,602 Days
• Field of Search: None
• 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 sequences by hybridization, comprising:

on a specifically programmed computer,

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

(b) selecting an oligonucleotide sequence specifically binding to a target sequence from the first target sequence group as a probe sequence, wherein the oligonucleotide sequence does not cross hybridize with other target sequences in the first target sequence group;

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

(d) selecting an oligonucleotide sequence specifically binding to a target sequence from the second target sequence group as a probe sequence, wherein the oligonucleotide sequence does not cross hybridize with other target sequences in the second target sequence group;

(e) repeating operations (c) and (d) until each target sequence in the plurality of target sequences has a specifically binding probe sequence or until it is impossible to select a specifically binding probe sequence for each target sequence in the plurality because of high sequence homology among a subset of the target sequences in the plurality, and

wherein when it is impossible to select a specifically binding probe sequence for each target sequence in the plurality because of high sequence homology among a subset of the target sequences, a sequence present in common in the subset, but not present in the other target sequences of the plurality, or the complementary sequence thereof, is selected as a probe sequence; and

(f) displaying the selected probe sequences to a user.

3. The method according to claim 1, further comprising

immobilizing probes consisting of the selected probe sequences on a substrate to obtain a micro array.

2. A computer readable medium on which a program is recorded for executing a method, the method comprising

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

(b) selecting an oligonucleotide sequence specifically binding to a target sequence from the first target sequence group as a probe sequence, wherein the oligonucleotide sequence does not cross hybridize with other target sequences in the first target sequence group;

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

(d) selecting an oligonucleotide sequence specifically binding to a target sequence from the second target sequence group as a probe sequence, wherein the oligonucleotide sequence does not cross hybridize with other target sequences in the second target sequence group;

(e) repeating operations (c) and (d) until each target sequence in the plurality of target sequences has a specifically binding probe sequence or until it is impossible to select a specifically binding probe sequence for each target sequence in the plurality because of high sequence homology among a subset of the target sequences in the plurality, and

wherein when it is impossible to select a specifically binding probe sequence for each target sequence in the plurality because of high sequence homology among a subset of the target sequences, a sequence present in common in the subset target sequences, but not present in the other target sequences of the plurality, or the complementary sequence thereof, is selected as a probe sequence; and

displaying the selected probe sequences to a users,

wherein the computer readable medium is a device to store computer readable data.

4. The computer readable medium of claim 2, wherein the device consists of a read-only memory (ROM), a random-access memory (RANT), a CD-ROM, a magnetic tape, a floppy disk, or an optical data storage device.