System and method for computer-designing optimum oligo-nucleic acid sequences from nucleic acid base sequences, and oligo-nucleic acid array mounted with the designed oligo-nucleic acid sequences

• US 20020198666A1
• Filed: 06/19/2002
• Published: 12/26/2002
• Est. Priority Date: 06/20/2001
• Status: Abandoned Application

• Current Assignee: KABUSHIKIGAISHA DYNACOM
• Original Assignee: KABUSHIKIGAISHA DYNACOM
• Inventors: Miura, Junichiro, Aoki, Yoshiaki, Fujimiya, Hitoshi
• Application Number:
  US10/174,630
• Publication Number:
  US 20020198666A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

Abstract

A computer software program and a method are provided to design an optimum oligo-nucleic acid sequence candidate from a nucleic acid base sequence. The program comprises a first command for receiving and storing a specified tolerance of double-chain bond temperature; a second command for computing the double-chain bond temperature of a partial sequence at each length, as extending the length; and a third command for determining whether or not the double-chain bond temperature computed by the second command falls within the tolerance specified by the first command, and in case it falls within the range, for outputting the partial sequence with the length as an oligo-nucleic acid sequence candidate. Based on the inputted tolerance of double-chain bond temperature, oligo-nucleic acid sequences with various lengths that meet the double-chain bond temperature condition can be obtained. An oligo-nucleic acid array mounted with the designed oligo-nucleic acid sequences is also provided.

Claims

1. A computer software program for designing an optimum oligo-nucleic acid sequence candidate from a nucleic acid base sequence, said program comprising:

a first command for receiving and storing a specification for a tolerance of double-chain bond temperature;

a second command for computing the double-chain bond temperature of a partial sequence at each length as extending the length of the partial sequence in said nucleic acid base sequence; and

a third command for determining whether or not the double-chain bond temperature computed by the second command falls within the tolerance obtained by the first command, and, if it does, for outputting the partial sequence of the length as an oligo-nucleic acid sequence candidate.

2. The computer software program according to claim 1,

wherein the second command successively shifts a starting point of the partial sequence for which the double-chain bond temperature is obtained in said nucleic acid sequences, and extends the length of the partial sequence from the shifted starting point.

3. The computer software program according to claim 2,

wherein the second command, when the third command determines that the double-chain bond temperature of the partial sequence is outside of the tolerance, shifts the starting point to the next point without extending the length any longer.

4. The computer software program according to claim 1,

said program further comprises:

a fourth command for displaying a plurality of oligo-nucleic acid sequence candidates outputted by the third command.

5. The computer software program according to claim 1,

said program further comprises:

a fifth command for comparing homomeric genes among a plurality of nucleic acid sequences and for identifying sequence parts specific and non-specific to each nucleic acid sequence, whereby the second command successively shifts a starting point of said specific sequence part in the partial sequence for which the double-chain bond temperature is obtained, and extends the length of the partial sequence from the shifted starting point.

6. The computer software program according to claim 5,

wherein the second command, when the third command determines that the double-chain bond temperature of the partial sequence is outside of the tolerance, shifts the starting point to the next point without extending the length any longer.

7. The computer software program according to claim 5,

wherein the second command further comprises a sixth command, which, when the extended partial sequence contains said non-specific sequence parts, determines whether to compute the double-chain bond temperature of said partial sequence or to set it as an oligo-nucleic acid sequence candidate;

and the second command, when the sixth command determines that no double-chain bond temperature is to be computed or no oligo-nucleic acid sequence candidate is to be set, shifts the starting point of said partial sequence to the beginning of the next specific sequence part.

8. The computer software program according to claim 7,

wherein the sixth command determines, based on the ratio of the specific sequence parts and the non-specific sequence parts or the respective sequence numbers contained in said extended partial sequence, whether to compute the double-chain bond temperature of said extended partial sequence or to set it as an oligo-nucleic acid sequence candidate.

9. The computer software program according to claim 7,

wherein the fourth command, when said non-specific sequence parts are contained in the partial sequence that falls within the tolerance of the double-chain bond temperature, outputs the partial sequence as a low-grade oligo-nucleic acid sequence candidate.

10. The computer software program according to claim 5,

wherein the second command, when no partial sequence with the length that has the double-chain bond temperature within the tolerance can be obtained from each specific sequence part, extends the length of the partial sequence to the non-specific sequence parts, and outputs the partial sequence that falls within the tolerance of the double-chain bond temperature as a low-grade oligo-nucleic acid sequence candidate.

11. A method for designing an optimum oligo-nucleic acid sequence candidate from a nucleic acid base sequence, said method comprising the steps of:

(a) specifying a tolerance of double-chain bond temperature;

(b) computing, within said nucleic acid base sequence, the double-chain bond temperature of a partial sequence at each length as extending the length; and

(c) determining whether or not the double-chain bond temperature computed by said computing means falls within the tolerance specified by said specifying means, and if it does, outputting the partial sequence of the length as an oligo-nucleic acid sequence candidate.

12. The method according to claim 11,

wherein Step (b) successively shifts a starting point of the partial sequence for which the double-chain bond temperature is obtained in said nucleic acid sequence, and extends the length of the partial sequence from the shifted starting point.

13. An oligo-nucleic acid array mounted with a plurality of oligo-nucleic acids having sequence lengths designed so as to have a predetermined double-chain bond temperature.