Signal processing method for determining base sequence of nucleic acid

• US 4,972,325 A
• Filed: 03/30/1987
• Issued: 11/20/1990
• Est. Priority Date: 03/29/1986
• 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: Hara, Makoto
• Primary Examiner(s): Lall, Parshotam S.
• Assistant Examiner(s): RAMIREZ, ELLIS B
• Application Number:
  US07/031,841
• Time in Patent Office: 1,331 Days
• Field of Search: 364/497, 364/496, 364/413.01, 364/413.13, 382/6, 435/6, 935/77, 358/111
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 27/44717 Arrangements for investigating the separated zones, e.g. localising zones
• 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) preparing one-dimensional waveform composed of position along the resolving direction and signal level for each resolved row;

(2) dividing the one-dimensional waveform into at least two intervals; and

(3) smoothing the one-dimensional waveform in every interval through a smoothing means having different characteristics.

Claims

1. A signal processing method for determining base sequence of nucleic acids by subjecting to signal processing 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 the steps of:

(1) generating a one-dimensional waveform composed of position along the resolving direction and signal level for each resolved row;

(2) selecting at least two intervals along the one-dimensional waveform;

(3) subjecting the digital signals in each said interval to smoothing processing using a moving average filter having a mask size that is varied for each said interval; and

(4) subjecting the smoothing processed digital signals to further processing, thereby detecting and sequencing bands corresponding to the sequence of bases in said nucleic acids.

2. The signal processing method as claimed in claim 1, wherein the mask size of said moving average filter is varied in every interval in the step (3).

3. The signal processing method as claimed in claim 2, wherein the mask size of said moving average filter is enlarged as the resolving distance is long in the step (3).

4. The signal processing method as claimed in claim 1, wherein said 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.

5. 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 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.

6. The signal processing method as claimed in claim 1, wherein said digital signals corresponding to the autoradiograph as obtained by placing the support medium and a radiosensitive material together in layers to record the autoradiograph of the resolved rows on the radiosensitive material as a visible image and photoelectrically reading out the autoradiograph visualized on said radiosensitive material.

7. A signal processing method for determining base sequence of nucleic acids by subjecting to signal processing 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 the steps of:

(1) generating a one-dimensional waveform composed of position along the resolving direction and signal level for each resolved row;

(2) selecting at least two intervals in the resolving direction along the one-dimensional waveform thus generated;

(3) processing each of said intervals with a smoothing means for smoothing processing the digital signals in each said interval according to spaces of bands in each said interval;

(4) detecting the sequence of bands in each resolved row; and

(5) determining said base sequence from the detected band sequence.

8. The signal processing method as claimed in claim 7, wherein said smoothing means is a weighted mean filter in the step (3).

9. The signal processing method as claimed in claim 7, wherein said smoothing means is a filter having low-pass characteristics in the step (3).

10. The signal processing method as claimed in claim 7, wherein said 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.

11. The signal processing method as claimed in claim 7, 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 resolved rows on the phosphor sheet as an energystored image, irradiating said phosphor sheet with stimulating rays and photoelectrically detecting the autoradiograph as stimulated emission.

12. The signal processing method as claimed in claim 7, wherein said digital signals corresponding to the autoradiograph are obtained by placing the support medium and a radiosenstive material together in layers to record the autoradiograph of the resolved rows on the radiosensitive material as a visible image and photoelectrically reading out the autoradiograph visualized on said radiosensitive material.