Claims for Patent: 7,698,069

Summary for Patent: 7,698,069

Title:	Method for designing primer for realtime PCR
Abstract:	A method for designing a primer for real-time PCR comprises retrieving a primer set using a known primer search algorithm and based on primer design conditions, visually displaying the retrieved primer set together with its splicing information and base sequence, narrowing the primer set using narrowing conditions, and visually displaying a narrowed primer set together with its splicing information and base sequence.
Inventor(s):	Yamamoto; Takamune (Tokyo, JP)
Assignee:	Hitachi Software Engineering Co., Ltd. (Kanagawa, JP)
Application Number:	11/185,892
Patent Claims:	1. A method for designing a primer for real-time PCR and implemented on a computer suitably configured and programmed to implement said method, comprising: a file selection step for entering a base sequence data file regarding a target gene; a determining step for determining whether or not said base sequence data file contains splicing information; a splicing information calculation step for calculating splicing information if it is determined in said determination step that splicing information is not contained; a parameter input step for inviting and receiving entries of primer design conditions by displaying splicing information which includes a length of an intron sequence removed by splicing and a position of binding by splicing in a schematic fashion; a first primer design step for designing primer sets using a known primer search algorithm and in accordance with said primer design conditions and displaying a screen for inviting and receiving entries of conditions for narrowing designed results; a narrowing step for narrowing the designed results in accordance with said conditions for narrowing designed results if an indication for narrowing designed results is entered into the computer; a detailed information display step for displaying a detailed information screen which includes a field for displaying said splicing information which includes the length of intron sequence removed by splicing and the position of binding by splicing in a schematic fashion, a field for displaying position information regarding a plurality of primer sets which include a plurality of primers on the nonsense strand side each relative to one primer on sense strand side, and a field for displaying detailed information of primer sets as selected in said field for displaying the position information regarding a plurality of primer sets; a second primer designing step for designing a primer for preparing an analytical curve-creating template if an indication for designing primer sets for preparing an analytical curve-creating template is entered in the computer; and a primer information output step for output information of the primer sets as designed to a file. 2. The method for designing a primer for real-time PCR according to claim 1, wherein said primer design conditions include the exon numbers on the left and right sides of intron, or the intron number between exons. 3. The computer implemented method for designing a primer for real-time PCR according to claim 1, wherein the second primer set designing step designs the primer set for preparing a template for creating an analytical curve by performing a known primer search algorithm while excluding an area sandwiched between the selected primer set in said field for displaying detailed information of primer sets in said detailed information screen. 4. The computer implemented method for designing a primer for real-time PCR according to claim 1, wherein the splicing information calculation step involves: entering a genomic DNA base sequence, while the base sequence being an mRNA base sequence; processing the base sequence as a character string, substituting an initial value of zero in a variable "DNA position" and a variable "mRNA position," and entering an initial value of zero in a variable "exon number" which counts the number of exons; substituting ten characters from the "mRNA position" in the mRNA base sequence in a character string "Searched sequence"; retrieving sequences corresponding to the genomic DNA base sequence from the "DNA position," and obtaining all mRNA base sequences included in the genomic DNA base sequence by splicing; determining whether there is one of the mRNA base sequences corresponding to the base sequence: if no, terminating the splicing information calculation step; if yes, using a subscript of a corresponding letter in the genomic DNA base sequence as a corresponding position, substituting a corresponding letter into a variable "exon start position" and the "DNA position," and incrementing the "exon number", the "mRNA position" and the "DNA position"; comparing letter by letter starting from a letter following the "DNA position" in the genomic DNA base sequence with a letter in the "mRNA position" in the mRNA base sequence, if the letters correspond with each other, incrementing the "mRNA position" and the "DNA positiont"; substituting the "DNA position" into a variable "exon end position," and adding the "exon number," the "exon start position," and the "exon end position" into the splicing information; and determining whether the "mRNA position" is at the end of the mRNA base sequence: if not, returning to the step of substituting ten characters, if yes, outputting the splicing information.

Details for Patent 7,698,069

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	For Injection	103132	06/04/1986		2024-09-01
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	For Injection	103132			2024-09-01
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	Injection	103132			2024-09-01