Method for analyzing autoradiograph for determining base sequence of nucleic acid

• US 4,982,326 A
• Filed: 10/04/1989
• Issued: 01/01/1991
• Est. Priority Date: 03/05/1986
• Status: Expired due to Term

• Current Assignee: Fuji Photo Film Co Limited (Fujifilm Holdings Corporation)
• Original Assignee: Fuji Photo Film Co Limited (Fujifilm Holdings Corporation)
• Inventors: Kaneko, Takashi
• Primary Examiner(s): Jablon, Clark A.
• Application Number:
  US07/420,603
• Time in Patent Office: 454 Days
• Field of Search: 364/413.01, 935/77, 935/78, 935/86, 935/87, 435/6, 435/808
• US Class Current: 435/5
• CPC Class Codes: G01N 27/44717 Arrangements for investigating the separated zones, e.g. localising zones

Abstract

A method of analyzing an autoradiograph of plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in one-dimensional direction on a support medium, to determine the base sequence of nucleic acids by:

(1) electrically displaying the autoradiograph as an image on a screen on the basis of digital signals corresponding to said autoradiograph;

(2) displaying a read cursor on the screen; and

(3) displaying a name of a base to which a band is assigned on the screen, which is determined by using the read cursor, together with the read cursor. A method of analyzing an autoradiograph which comprises recording and storing pattern information, cursor information and base sequence information, and a method which comprises verifying and/or correcting the determined sequence of bands are also disclosed.

Claims

1. A method of analyzing an autoradiograph of plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises steps of:

(1) obtaining digital signals corresponding to the autoradiograph by placing the support medium and a stimulable phosphor sheet comprising a stimulable phosphor together in layers to record the autoradiograph of plural resolved rows on the phosphor sheet as an energy-stored image, irradiating said phosphor sheet with stimulating rays and photoelectrically detecting the autoradiograph as stimulated emission; and

electrically displaying the autoradiograph as an image on a screen on the basis of digital signals corresponding to said autoradiograph;

(2) preparing and displaying a read cursor on the screen; and

(3) determining the name of a base to which a band is assigned by using the read cursor and displaying the name of said base on the screen together with the read cursor.

2. The method of analyzing an autoradiograph as claimed in claim 1, wherein said read cursor is displayed in the form of a broken line or a curved line as to allow the cursor to traverse the resolved rows along a band of each row in the second step.

3. The method of analyzing an autoradiograph as claimed in claim 2, wherein said read cursor is prepared by drawing straight lines or an arc which passes through at least one given position according to input of said position in the second step.

4. The method of analyzing an autoradiograph as claimed in claim 3, wherein said position is inputted by using a pointing device.

5. The method of analyzing an autoradiograph as claimed in claim 4, wherein said pointing device is a mouse cursor.

6. The method of analyzing an autoradiograph as claimed in claim 1, wherein said base name is displayed in the form of a character and/or a symbol at the end of the read cursor in the third step.

7. The method of analyzing an autoradiograph as claimed in claim 1, wherein said autoradiograph is displayed as a shading image, a binary image or an image represented by multi-displaying two-dimensional waveforms composed of position along the resolving direction and image density at regular intervals in a direction perpendicular to the resolved direction in the first step.

8. The method of analyzing an autoradiograph as claimed in claim 1, wherein a read cursor to be used in reading a band subsequent to any read cursor having assigned a band to a base displayed in the third step, is distinguishable in appearance from such prior read cursor.

9. The method of analyzing an autoradiograph as claimed in claim 1, wherein a name of base to which a band is assigned displayed subsequent to any name of base to which a band has been assigned displayed in the third step, is distinguishable in appearance from such prior name of base.

10. A method of analyzing an autoradiograph of plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in a one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises the steps of:

(1) obtaining digital signals corresponding to an autoradiograph and electrically displaying the autoradiograph as an image on a screen on the basis of said digital signals;

wherein said digital signals are obtained by placing the support medium and a radiosensitive material together in layers to record the autoradiograph of plural resolved rows on the radiosensitive material as a visible image and photoelectrically reading out the autoradiograph visualized on said radiosensitive material;

(2) preparing and displaying a read cursor on the screen; and

(3) determining the name of a base to which a band is assigned by using the read cursor and displaying the name of said base on the screen together with said read cursor.

11. A method of analyzing an autoradiograph of a resolved pattern comprising plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in a one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises separating information on said autoradiograph and the base sequence of nucleic acid determined on the basis of the autoradiograph into the following three kinds of information:

(1) information on the autoradiograph of the resolved pattern;

(2) information on plural read cursors which pass through bands on the autoradiograph and indicate relative positions on the bands; and

(3) information on the sequence of bases to which the bands on the autoradiograph are assigned;

establishing a correspondence between the pattern information (1) and the cursor information (2) and a correspondence between the cursor information (2) and the base sequence information (3), wherein said information is in the form of digital signals corresponding to the autoradiograph obtained by placing the support medium and a stimulable phosphor sheet comprising a stimulable phosphor together in layers to record the autoradiograph of plural resolved rows on the phosphor sheet as an energy-stored image, irradiating said phosphor sheet with stimulating rays and photoelectrically detecting the autoradiograph as stimulated emission; and

recording and storing said information.

12. The method of analyzing an autoradiograph as claimed in claim 11, wherein said correspondence between the pattern information and the cursor information is established by coordinates, and said correspondence between the cursor information and the base sequence information is established by order.

13. The method of analyzing an autoradiograph as claimed in claim 11, wherein said pattern information, cursor information and base sequence information are stored in a secondary storage.

14. The method of analyzing an autoradiograph as claimed in claim 11, wherein said pattern information, cursor information and base sequence information are recorded on the same recording medium.

15. The method of analyzing an autoradiograph as claimed in claim 11, wherein said pattern information includes a shading image, a binary image or an image represented by multi-displaying two-dimensional waveforms composed of position along the resolving direction and image density at regular intervals in a direction perpendicular to the resolved direction.

16. The method of analyzing an autoradiograph as claimed in claim 11, wherein said cursor information includes a plurality of broken lines or curved lines which traverse the resolved rows along a band of each row.

17. The method of analyzing an autoradiograph as claimed in claim 11, wherein said base sequence information includes a series of characters and/or symbols.

18. A method of analyzing an autoradiograph of a resolved pattern comprising plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in a one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises separating information on said autoradiograph and the base sequence of nucleic acid determined on the basis of the autoradiograph into the following three kinds of information:

(1) information on the autoradiograph of the resolved pattern;

(2) information on plural read cursors which pass through bands on the autoradiograph and indicate relative positions on the bands; and

(3) information on the sequence of bases to which the bands on the autoradiograph are assigned;

establishing a correspondence between the pattern information (1) and the cursor information (2) and a correspondence between the cursor information (2) and the base sequence information (3), wherein digital signals corresponding to the autoradiograph are obtained by placing the support medium and a radiosensitive material together in layers to record the autoradiograph of plural resolved rows on the radiosensitive material as a visible image and photoelectrically reading out the autoradiograph visualized on said radiosensitive material; and

recording and storing said information.

19. A method of analyzing an autoradiograph of a resolved pattern comprising plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in a one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises the steps of:

(1) determining a sequence of bands by subjecting digital signals corresponding to the autoradiograph to signal processing and electrically displaying an autoradiograph in which sequence of bands has been determined as an image on a screen on the basis of digital signals corresponding to said autoradiograph;

(2) preparing and displaying a read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to traverse the resolved rows and to pass through one band position according to input for verification of the band'"'"'s sequence;

(3) verifying the sequence of the band and displaying the base name of said band together on the screen;

(4) preparing and displaying another read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to pass through a band position adjacent to the band to which the cursor is fixed in step (2) according to input for verification of the band'"'"'s sequence;

(5) verifying the sequence of the band and displaying the base name of said band together on the screen; and

(6) repeating step (4) to verify the determined sequence of the bands on the autoradiograph.

20. The method of analyzing an autoradiograph as claimed in claim 19, wherein said band to which the cursor is fixed in step 2 is the lowermost band and the sequence of the bands is verified in order from the lowermost band in steps (2) through (5).

21. The method of analyzing an autoradiograph as claimed in claim 19, wherein said input for verification of the band'"'"'s sequence in steps (2) through (5) is based on the determined sequence of the bands.

22. The method of analyzing an autoradiograph as claimed in claim 19, wherein said read cursor is displayed in the form of a broken line or a curved line in steps (2) through (5).

23. The method of analyzing an autoradiograph as claimed in claim 19, wherein said autoradiograph of the resolved pattern displayed as an image, said plural read cursors fixed to the autoradiograph and the verified sequence of the bands are separated as pattern information (1), cursor information (2) and base sequence information (3) from one another, and said information is recorded and stored in such a manner as to establish a correspondence between (1) and (2) and a correspondence between (2) and (3).

24. The method of analyzing an autoradiograph as claimed in claim 19, wherein said autoradiograph is displayed as a shading image, a binary image or an image represented by multi-displaying two-dimensional waveforms composed of position along the resolving direction and image density at regular intervals in a direction perpendicular to the resolved direction in step (1).

25. A method of analyzing an autoradiograph of a resolved pattern comprising plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises steps of:

(1) obtaining digital signals corresponding to an autoradiograph and electrically displaying the autoradiograph in which sequence of bands has been determined as an image on a screen on the basis of digital signals corresponding to said autoradiograph, wherein said digital signals are obtained by placing the support medium and a stimulable phosphor sheet comprising a stimulable phosphor together in layers to record the autoradiograph of plural resolved rows on the phosphor sheet as an energy-stored image, irradiating said phosphor sheet with stimulating rays and photoelectrically detecting the autoradiograph as stimulated emission;

(2) preparing and displaying a read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to traverse the resolved rows and to pass through one band position according to input for verification of the band'"'"'s sequence;

(3) verifying the band'"'"'s sequence and displaying the base name of said band together on the screen;

(4) preparing and displaying a read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to pass through a band position adjacent to the band to which the cursor is fixed in the second step according to input for verification of the band'"'"'s sequence,

(5) verifying the band'"'"'s sequence and displaying the base name of said band together on the screen; and

(6) repeating step (4) and (5) to verify the determined sequence of the bands on the autoradiograph.

26. A method of analyzing an autoradiograph of a resolved pattern comprising plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises steps of:

(1) obtaining digital signals corresponding to an autoradiograph and electrically displaying the autoradiograph in which sequence of bands has been determined as an image on a screen on the basis of digital signals corresponding to said autoradiograph;

wherein said digital signals are obtained by placing the support medium and a radiosensitive material together in layers to record the autoradiograph of plural resolved rows on the radiosensitive material as a visible image and photoelectrically reading out the autoradiograph visualized on said radiosensitive material;

(2) preparing and displaying a read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to traverse the resolved rows and to pass through one band position according to input for verification of the band'"'"'s sequence;

(3) verifying the band'"'"'s sequence and displaying the base name of said band together on the screen;

(4) preparing and displaying a read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to pass through a band position adjacent to the band to which the cursor is fixed in the second step according to input for verification of the band'"'"'s sequence and displaying the base name of said band together on the screen; and

(6) repeating step (4) and (5) to verify the determined sequence of the bands on the autoradiograph.

27. A method of analyzing an autoradiograph of a resolved pattern comprising plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises the steps of:

(1) determining the sequence of bands by subjecting digital signals corresponding to an autoradiograph to signal processing and electrically displaying the autoradiograph in which the sequence of bands has been determined as an image on a screen on the basis of digital signals corresponding to said autoradiograph;

(2) preparing and displaying a read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to traverse the resolved rows and to pass through one band position according to input for verification of the band'"'"'s sequence;

(3) verifying the band'"'"'s sequence and displaying the base name of said band together on the screen;

(4) preparing and displaying a second read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to pass through a band position adjacent to the band to which the cursor is fixed in the second step according to input for verification of the band'"'"'s sequence

(5) verifying the band'"'"'s sequence and displaying the base name of said band together on the screen;

(6) deleting, adding or changing the read cursor and/or the base name displayed in step (4) according to input, when there is inputted information on the basis of the display screen;

(7) verifying the determined sequence of the bands by repeating in order steps (4), (5) and (6); and

(8) correcting the determined sequence of the bands as required.

28. The method of analyzing an autoradiograph as claimed in claim 27, wherein said band to which the cursor is fixed in step (2) is the lowermost band and the sequence of the bands is verified and corrected in order from the lowermost band in steps (2) through (8).

29. The method of analyzing an autoradiograph as claimed in claim 27, wherein said input for verification of the band'"'"'s sequence in steps (2), (3) and (4) is based on the determined sequence of the bands.

30. The method of analyzing an autoradiograph as claimed in claim 27, wherein said read cursor is displayed in the form of a broken line or a curved line in steps (2), (3) and (4).

31. The method of analyzing an autoradiograph as claimed in claim 27, wherein said autoradiograph of the resolved pattern displayed as an image, said plural read cursors fixed to the autoradiograph, and the verified and corrected sequence of the bands are separated as pattern information (1), cursor information (2) and base sequence information (3) from one another, and said information is recorded and stored in such a manner as to establish a correspondence between (1) and (2) and a correspondence between (2) and (3).

32. The method of analyzing an autoradiograph as claimed in claim 27, wherein said autoradiograph is displayed as a shading image, a binary image or an image represented by multi-displaying two-dimensional waveforms composed of position along the resolving direction and image density at regular intervals in a direction perpendicular to the resolved direction in step (1).

33. A method of analyzing an autoradiograph of a resolved pattern comprising plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in a one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises the steps of:

(1) obtaining digital signals and electrically displaying an autoradiograph in which a sequence of bands has been determined as an image on a screen on the basis of said digital signals corresponding to said autoradiograph, wherein said digital signals are obtained by placing the support medium and a stimulable phosphor sheet comprising a stimulable phosphor together in layers to record the autoradiograph of plural resolved rows on the phosphor sheet as an energy-stored image, irradiating said phosphor sheet with stimulating rays and photoelectrically detecting the autoradiograph as stimulated emission;

(2) preparing and displaying a read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to traverse the resolved rows and to pass through one band position according to input for verification of the band'"'"'s sequence, and displaying the base name of said band together on the screen;

(3) preparing and displaying a second read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to pass through a band position adjacent to the band to which the cursor is fixed in step (2) according to input for verification of the band'"'"'s sequence,

(4) verifying the band'"'"'s sequence and displaying the base name of said band on the screen;

(5) deleting, adding or changing the read cursor and/or the base name displayed in step (4) according to input, when there is inputted information on the basis of the display screen;

(6) verifying the determined sequence of the bands by repeating in order steps (3), (4) and (5); and

(7) correcting the determined sequence of the bands as required.

34. A method of analyzing an autoradiograph of a resolved pattern comprising plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in a one-dimensional direction on a support medium, to determine the base sequence of nucleic acids,

which comprises the steps of:

(1) obtaining digital signals and electrically displaying an autoradiograph in which sequence of bands has been determined as an image on a screen on the basis of said digital signals corresponding to said autoradiograph, wherein said digital signals are obtained by placing the support medium and a radiosensitive material together in layers to record the autoradiograph of plural resolved rows on the radiosensitive material as a visible image and photoelectrically reading out the autoradiograph visualized on said radiosensitive material;

(2) preparing and displaying a read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to traverse the resolved rows and to pass through one band position according to input for verification of the band'"'"'s sequence, and displaying the base name of said band on the screen;

(3) preparing and displaying a second read cursor on the screen to fix the cursor to the autoradiograph so as to allow the cursor to pass through a band position adjacent to the band to which the cursor is fixed in step (2) according to input for verification of the band'"'"'s sequence,

(4) verifying the band'"'"'s sequence and displaying the base name of said band on the screen;

(5) deleting, adding or changing the read cursor and/or the base name displayed in the step (4) according to input, when there is inputted information on the basis of the display screen;

(6) verifying the determined sequence of the bands by repeating in order steps (3), (4) and (5); and

(7) correcting the determined sequence of bands as required.

35. A method of analyzing an autoradiograph of plural resolved rows which are formed by resolving base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in one-dimensional direction on a support medium to determine the base sequence of the nucleic acids in said fragments which comprises the steps of:

(1) obtaining digital signals corresponding to the autoradiograph and processing said digital signals to electrically display the autoradiograph as an image on a screen;

(2) preparing a read cursor by drawing straight lines or an arc which passes through at least one given position on said image and displaying said read cursor on said screen so that said read cursor is capable of traversing the resolved rows along a band of each row; and

(3) assigning to a band the name of a base, determining the name of said base with said read cursor, and displaying the same of said base and said read cursor on the screen.