Signal processing method for determining base sequence of nucleic acid

• US 4,941,092 A
• Filed: 05/23/1986
• Issued: 07/10/1990
• Est. Priority Date: 05/23/1985
• 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: Hashiue, Masakazu, Hara, Makoto, Tanaka, Kazuyoshi
• Primary Examiner(s): Fleming, Michael R.
• Assistant Examiner(s): Bui, Kim Thanh T.
• Application Number:
  US06/866,355
• Time in Patent Office: 1,509 Days
• Field of Search: 364/413.01, 364/413.15, 382/6, 935/77, 435/6
• US Class Current: 382/129
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01T 1/2942 using autoradiographic methods

Abstract

A signal processing method for determining base sequence of nucleic acids by subjecting digital signals to signal processing, said digital signals corresponding to an autoradiograph of plural resolved rows which are formed by resolving a mixture of base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in one-dimensional direction on a support medium,

which comprises steps of:

(1) detecting at least two bands continuously in the lower part of each resolved row and numbering the bands consecutively in order from the lower end;

(2) obtaining correlation of a distance between the detected bands in the resolving direction with the band'"'"'s number and predicting positions of undetected bands in the resolving direction from the correlation;

(3) detecting at least one band on the resolved rows on the basis of the predicted positions and numbering the bands consecutively;

(4) obtaining the correlation of the distance between the bands with the band'"'"'s number for the already detected bands including the band newly detected in the step (3), and predicting positions of undetected bands from the correlation; and

(5) repeating in order the steps (3) and (4) to thereby detect all bands on the resolved rows.

Claims

1. A signal processing method for determining base sequence of nucleic acids by subjecting digital signals to signal processing, said digital signals corresponding to an autoradiograph of plural resolved rows which are formed by resolving a mixture of base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in a one-dimensional resolving direction on a support medium,

which comprises steps of:

(1) detecting at least two bands continuously in the lower part of each resolved row and numbering the bands consecutively in order from the lower end;

(2) obtaining correlation of a distance between the detected bands in the resolving direction with the band'"'"'s number and predicting positions of undetected bands in the resolving direction from the correlation;

(3) detecting at least one band on the resolved rows on the basis of the predicted positions and numbering the band consecutively;

(4) obtaining the correlation of the distance between the bands with the band'"'"'s number for the already detected bands including the band newly detected in the step (3), and predicting positions of undetected bands from the correlation; and

(5) repeating in order the steps (3) and (4) to thereby detect all bands on the resolved rows.

2. The signal processing method as claimed in claim 1, wherein said bands are detected by extracting digital signals along the resolving direction of each resolved row and then finding out positions where level of the extracted signal is maximum, in said step (1).

3. The signal processing method as claimed in claim 1, wherein said correlation of the distance between the bands with the band'"'"'s number is obtained as a regression line or a regression curve, and said positions of undetected bands are predicted by extrapolating the regression line or the regression curve, in said step (2).

4. The signal processing method as claimed in claim 1, wherein said correlation of the distance between the bands with the band'"'"'s number is obtained for the already detected bands including the band newly detected in the step (3), wherein a band having the lower number is identified and said band having the lower number is excluded in said step (4).

5. The signal processing method as claimed in claim 1, wherein said correlation of the distance between the bands with the band'"'"'s number is obtained every time detecting a band, and all bands are detected one by one on the resolved rows, in said steps (3) to (5).

6. The signal processing method as claimed in claim 1, wherein said correlation of the distance between the bands with the band'"'"'s number is obtained every time detecting a given number of bands, and all bands are detected by the given number on the resolved rows, in said steps (3) to (5).

7. The signal processing method as claimed in claim 1, wherein before the step (1), correction for resolved distance is made on each resolved row on the basis of ratio of the resolved distance between the rows, said ratio being determined by detecting inclination of at least one band to the resolving direction for each row.

8. The signal processing method as claimed in claim 1, wherein before the step (1), correction for resolved position is made on each resolved row on the basis of difference in resolved distance between the rows, said difference being determined by detecting at least two bands in the lower part of each row, numbering the bands consecutively in order from the lower end and then obtaining correlation between the band'"'"'s number and the resolved distance thereof for each row.

9. The signal processing method as claimed in claim 1, wherein the mixture of the base-specific DNA fragments consists of the four groups of:

(1) guanine-specific DNA fragments;

(2) adenine-specific DNA fragments;

(3) thymine-specific DNA fragments; and

(4) cytosine-specific DNA fragments;

and the resolved rows consist of four rows formed by resolving each of said four groups of the base-specific DNA fragments on the support medium.

10. The signal processing method as claimed in claim 1, wherein said digital signals corresponding to the autoradiograph are obtained by placing the support medium and a stimulable phosphor sheet comprising a stimulable phosphor together in layers to record the autoradiograph of the 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.

11. The signal processing method as claimed in claim 1, wherein said 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 the plural resolved rows on the radiosensitive material as a visible image and photoelectrically reading out the autoradiograph visualized on said radiosensitive material.

12. A signal processing method for determining base sequence of nucleic acids by subjecting digital signals to signal processing, said digital signals corresponding to an autoradiograph of plural resolved rows which are formed by resolving a mixture of base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in a one-dimensional resolving direction on a support medium,

which comprises steps of:

(1) detecting at least two bands continuously in the lower part of each resolved row and numbering the bands consecutively in order from the lower end;

(2) obtaining correlation between a resolved distance of the detected band and the band'"'"'s number and predicting positions of undetected bands in the resolving direction from the correlation;

(3) detecting at least one band on the resolved rows on the basis of the predicted positions and numbering the band consecutively;

(4) obtaining the correlation of the resolved distance of the band and the band'"'"'s number for the already detected bands including the band newly detected in the step (3), and predicting positions of undetected bands from the correlation; and

(5) repeating in order the steps (3) and (4) to thereby detect all bands on the resolved rows.

13. The signal processing method as claimed in claim 12, wherein said bands are detected by extracting digital signals along the resolving direction of each resolved row and then finding out positions where level of the extracted signal is maximum, in said step (1).

14. The signal processing method as claimed in claim 12, wherein said correlation of the resolved distance of the band with the band'"'"'s number is obtained as a regression line or a regression curve, and said positions of undetected bands are predicted by extrapolating the regression line or the regression curve, in said step (2).

15. The signal processing method as claimed in claim 12, wherein said correlation of the resolved distance of the band with the band'"'"'s number is obtained for the already detected bands including the band newly detected in the step (3) and excluding the band having the lower number, in said step (4).

16. The signal processing method as claimed in claim 12, wherein said correlation of the resolved distance of the band with the band'"'"'s number is obtained every time detecting a band, and all bands are detected one by one on the resolved rows, in said steps (3) to (5).

17. The signal processing method as claimed in claim 12, wherein said correlation of the resolved distance of the band with the band'"'"'s number is obtained every time detecting a given number of bands, and all bands are detected by the given number on the resolved rows, in said steps (3) to (5).

18. The signal processing method as claimed in claim 12, wherein before the step (1), correction for resolved distance is made on each resolved row on the basis of ratio of the resolved distance between the rows, said ratio being determined by detecting inclination of at least one band to the resolving direction for each row.

19. The signal processing method as claimed in claim 12, wherein before the step (1), correction for resolved position is made on each resolved row on the basis of difference in resolved distance between the rows, said difference being determined by detecting at least two bands in the lower part of each row, numbering the bands consecutively in order from the lower end and then obtaining correlation between the band'"'"'s number and the resolved distance thereof for each row.

20. The signal processing method as claimed in claim 12, wherein the mixture of the base-specific DNA fragments consists of the four groups of:

(1) guanine-specific DNA fragments;

(2) adenine-specific DNA fragments;

(3) thymine-specific DNA fragments; and

(4) cytosine-specific DNA fragments;

and the resolved rows consist of four rows formed by resolving each of said four groups of the base-specific DNA fragments on the support medium.

21. The signal processing method as claimed in claim 12, wherein said digital signals corresponding to the autoradiograph are obtained by placing the support medium and a stimulable phosphor sheet comprising a stimulable phosphor together in layers to record the autoradiograph of the 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.

22. The signal processing method as claimed in claim 12, wherein said 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 the plural resolved rows on the radiosensitive material as a visible image and photoelectrically reading out the autoradiograph visualized on said radiosensitive material.

23. A signal processing method for determining base sequence of nucleic acids by subjecting digital signals to signal processing, said digital signals corresponding to an autoradiograph of plural resolved rows which are formed by resolving a mixture of base-specific DNA fragments or base-specific RNA fragments labeled with a radioactive element in a one-dimensional resolving direction on a support medium,

which comprises steps of:

(1) detecting at least two bands continuously in the lower part of each resolved row and numbering the bands consecutively in order from the lower end;

(2) obtaining correlation of a distance between the detected bands in the resolving direction with the band'"'"'s number and predicting positions of undetected bands in the resolving direction from the correlation; and

(3) detecting al bands on the resolved rows on the basis of the predicted positions.

24. The signal processing method as claimed in claim 23, wherein said bands are detected by extracting digital signals along the resolving direction of each resolved row and then finding out positions where level of the extracted signal is maximum, in said step (1).

25. The signal processing method as claimed in claim 23, wherein said correlation of the distance between the bands with the band'"'"'s number is obtained as a regression line or a regression curve, and said positions of undetected bands are predicted by extrapolating the regression line or the regression curve, in said step (2).

26. The signal processing method as claimed in claim 23, wherein said bands are detected by finding out points or areas where signal level is not less than a threshold value and then deciding that the bands exist at the points or areas which correspond to the predicted positions of the undetected bands, in said step (3).

27. The signal processing method as claimed in claim 23, wherein before the step (1), correction for resolved distance is made on each resolved row on the basis of ratio of the resolved distance between the rows, said ratio being determined by detecting inclination of at least one band to the resolving direction for each row.

28. The signal processing method as claimed in claim 23, wherein before the step (1), correction for resolved position is made on each resolved row on the basis of difference in resolved distance between the rows, said difference being determined by detecting at least two bands in the lower part of each row, numbering the bands consecutively in order from the lower end and then obtaining correlation between the band'"'"'s number and the resolved distance thereof for each row.

29. The signal processing method as claimed in claim 23, wherein the mixture of the base-specific DNA fragments consists of the four groups of:

(1) guanine-specific DNA fragments;

(2) adenine-specific DNA fragments;

(3) thymine-specific DNA fragments; and

(4) cytosine-specific DNA fragments;

and the resolved rows consist of four rows formed by resolving each of said four groups of the base-specific DNA fragments on the support medium.

30. The signal processing method as claimed in claim 23, wherein said digital signals corresponding to the autoradiograph are obtained by placing the support medium and a stimulable phosphor sheet comprising a stimulable phosphor together in layers to record the autoradiograph of the 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.

31. The signal processing method as claimed in claim 23, wherein said 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 the plural resolved rows on the radiosensitive material as a visible image and photoelectrically reading out the autoradiograph visualized on said radiosensitive material.