Method and device for fragment trace data display in DNA base sequencing

In a DNA base sequencing, a consensus sequence is obtained by linking a plurality of DNA fragments obtained by a DNA sequencer, and a base sequence to be edited is determined in the consensus sequence. Then, a trace corresponding to the determined base sequence to be edited is identified among traces obtained by the DNA sequencer. The identified trace is displayed in correspondence with the base sequence to be edited. At this time, the base sequence to be edited is displayed so that an interval between bases becomes even.

BACKGROUND OF THE INVENTION 
1. Field of the Invention 
The present invention relates to a method for determining a base sequence 
of a DNA which is one type of nucleic acid, and more particularly to a 
method for displaying a base sequence trace (waveform) of a DNA fragment 
for use in a DNA base sequencing using a DNA sequencer. 
2. Description of the Related Art 
A constituent of a nucleic acid is a nucleotide, which is composed of a 
base, pentose, and phosphoric acid. The phosphoric acid and a nucleoside 
combine to form the nucleotide. Nucleosides are cross-linked by the 
phosphoric acid, so that a DNA (deoxyribonucleic acid) and an RNA 
(ribonucleic acid), which are polymers, are generated. 
The base forming the nucleic acid comprises two types, a purine and a 
pyrimidine. The purine comprises an adenine A and a guanine G, while the 
pyrimidine comprises a cytosine C and a thymine T. 
The DNA has a polynucleotide-chain structure, in which adenine A, guanine 
G, cytosine C, and thymine T are aligned as a string. If DNAs were 
extracted from one chromosome of a human cell and linked in sequence, they 
would extend for about one meter, in which three billion bases remain in 
sequence. 
Accordingly, determining a sequence of the four bases adenine A, guanine G, 
cytosine C, and the thymine T allows genetic information to be analyzed. 
The DNA sequencing technology for determining a base sequence progresses 
as techniques in other fields advance. Its progress correlates closely to 
progress made in technical fields such as the discoveries of restriction 
enzymes and enzymes related to nucleic acid, DNA cloning, 
nucleo-chemistry, etc. 
In recent years, computer technology is frequently applied to the DNA 
sequencing. Since the computer technology enables accumulation and entry 
of huge amounts of data beyond the capability of a human being, a computer 
is used as an essential tool for determining a base sequence. 
As described above, the DNA has a structure of a primary base sequence 
linked in the form of a chain. The DNA chain has directionality. That is, 
a base sequence ATGCACGA.fwdarw. is different from a base sequence 
ATGCACGA.rarw. (that is, AGCACGTA.fwdarw.). 
Both ends of the DNA chains are named. The end where a hydroxyl group is 
linked to a sugar at a location 3' is called the 3' end, while the other 
end where a phosphoric acid group is linked to a sugar at a location 5' is 
called the 5' end. Normally, a DNA chain is described so that the 5' and 
3' ends are arranged at the left and right sides respectively. 
The DNA exists in a double-stranded state where two complementary base 
sequences in different directions are united. There is a definite 
relationship between the two complementary base sequences which face each 
other. That is, the adenine A only faces the thymine T, while the guanine 
G only faces the cytosine C. An example of a double-stranded DNA is given 
below. 
ATGCATGCTAGCTAGCT.fwdarw.("a" strand) 
TACGTACGATCGATCGA.rarw.("b" strand) 
As shown above, the "a" strand pairs with the "b" strand. The "b" strand is 
complementary to the "a" strand. Accordingly, the "b" strand can be also 
represented as follows: 
AGCTAGCTAGCATGCAT.fwdarw. 
The DNA is genetically defined by making a pair of two complementary base 
sequences. If one of the two complementary base sequences is determined, 
the other of the two can be determined. This means that the base sequence 
of the DNA can be determined. 
For a DNA sequencer for automatically reading a base sequence of a DNA, the 
dideoxyn method or the Sanger method is used to determine a base sequence. 
Normally, when DNA synthesis is performed using a portion of one of the 
complementary double strands of a DNA as a primer for initiating the DNA 
synthesis, adding a dideoxynucleotide halts the DNA synthesis. As a 
result, fragments of the DNA having a variety of lengths can be obtained. 
Therefore, by adding the dideoxynucleotide corresponding to each of the 
bases G, A, T, and C at the time of DNA synthetic reaction, the DNA 
fragments having a variety of lengths whose chains are cleaved at each 
location of each of the bases, can be obtained. 
FIG. 1 is a schematic diagram showing a process for generating DNA 
fragments cleaved at locations of one particular nucleotide, the adenine A 
in this case. As shown in this figure, the chemical process for removing 
one nucleotide, that is, the adenine A from a DNA 1 whose 5' end is 
labelled with .sup.32 p, is performed. As a result, the DNA 1 is separated 
into radioactive labelled fragment 2 having a phosphoric acid group at the 
5' end on the left side of the figure and fragments 3 which are 
non-labelled. Then, these fragments are isolated by gel electrophoresis. 
The radioactive fragments 2 are detected at locations respectively 
corresponding to the lengths of the fragments (or molecular weights) by 
autoradiography. 
With the DNA sequencer, DNA fragments generated by a reaction of the 
dideoxyn method are fluorescence-marked. The DNA fragments having a 
variety of lengths of fluorescence-marked chains are isolated by a gel 
electrophoresis. For the DNA fragments electrophoresed in a gel, their 
fluorescent pigment is excitation-radiated at a certain location on the 
gel by laser irradiation, and detected by an optical detector. By 
detecting the fluorescence continuously and simultaneously with the 
electrophoresis, data of the electrophoretic patterns of DNA fragments 
corresponding to each of the bases G, A, T, and C, can be obtained. The 
data thus obtained is analyzed by a computer, and converted into base 
sequence data. 
Output data from the DNA sequencer includes a DNA base sequence itself, and 
trace data (waveform data) used to determine a base sequence. The trace 
data corresponds to data of a gel electrophoretic pattern, and a location 
of a peak in each of the traces (waveforms) of the bases G, A, T, and C 
corresponds to a location where a corresponding base exists. 
However, since the number of bases included in a base sequence of a DNA is 
generally very large, it is difficult to determine the whole of the base 
sequence at one time using the DNA sequencer. Accordingly, by separating a 
DNA to be determined into a plurality of fragments, determining a base 
sequence of each of the plurality of fragments, and linking the base 
sequences, the entire base sequence is determined. For the fragmentation, 
the DNA is fragmented by overlapping both ends of each of the fragments, 
and a base sequence of each of the fragments is obtained. 
For the process for determining a base sequence using the DNA sequencer, 
the number of bases read at one time is limited, as described above. 
Furthermore, the contents of read sequence data may be quite ambiguous 
depending on the accuracy of experiments conducted by using gel 
electrophoresis. 
FIG. 2 shows an output example of trace data obtained from a DNA sequencer. 
In each of the graphs shown in this figure, a vertical axis indicates 
fluorescent intensity, while numerical values on a horizonal axis indicate 
base numbers in a DNA sequence. Since traces can be enlarged for display 
depending on need as shown in the four graphs in this figure, the base 
sequence can be read corresponding to the peak locations of the respective 
traces in these graphs. 
For a DNA whose base sequence is desired to be determined as described 
above, an editing operation such as enlarging a fragment sequence, linking 
fragment sequences, removing a base which is difficult to be identified, 
inserting a base, depending on need, etc., is performed to assemble a base 
sequence. In this case, it is desirable that the editing and assembling 
operations be performed more accurately and more quickly to obtain a 
desired base sequence. 
When fragment data read by the DNA sequencer is linked or edited in order 
to assemble a base sequence, it is often the case that a character 
sequence is extracted from the data read by the sequencer to perform 
linking and editing operations, and at the same time, trace data is 
referenced, depending on need. Conventionally, only trace data 
corresponding to a fragment is displayed for referencing the trace data. 
Such a display does not enable a study by making a comparison between 
traces. As described above, peak intervals of trace data may differ 
depending on experimental data due to non-uniformity of quality of gels 
used in electrophoresis, slight differences in experimental conditions, 
etc. Therefore, as long as traces are simply displayed, there is a 
difficulty in finding visual correspondence between portions of traces to 
be compared, and the display is not helpful for accurately assembling a 
base sequence. 
Furthermore, as a molecular weight of a base increases in gel 
electrophoresis, a travel distance of the base becomes shorter, in a 
conventional method. As a result, base intervals corresponding to a trace 
become irregular. 
FIG. 3 shows a graph where such irregularities of base intervals exist. For 
example, the interval between base numbers 100 and 200 is different from 
that between base numbers 600 and 700 in this figure. That is, it 
indicates that the base intervals are not regular. Due to slight 
differences in experimental conditions, locations of traces corresponding 
to the same base number are different. Accordingly, with an editing 
operation using such a graph, a simple comparison between traces cannot 
easily be made. 
SUMMARY OF THE INVENTION 
The object of the present invention is to provide a method and a device for 
facilitating finding a correspondence between locations on traces 
(waveforms) to be compared, when trace data (waveform data) of respective 
fragments of a DNA are compared. Another object of the present invention 
is to determine a base sequence more accurately in a process for linking 
fragment data and an editing operation after linkage, according to the 
above described method and device. 
The method according to the present invention is a fragment trace data 
display method for determining a base sequence of the DNA based on traces 
representing base sequences of the plurality of fragments of the DNA 
obtained by an electrophoresis. This method includes the steps of: 
determining the base sequences of the plurality of fragments as fragment 
base sequences; obtaining a consensus sequence by linking the fragment 
base sequences; displaying the traces in correspondence with the consensus 
sequence; and determining the base sequence of the DNA by referencing the 
displayed traces in correspondence with the consensus sequence and editing 
the consensus sequence. The traces and the fragment base sequences are 
obtained as outputs from a DNA sequencer for determining the base sequence 
of the DNA. 
The fragment trace data display method may further include the steps of: 
providing location information indicating a location on a trace for a base 
included in a fragment base sequence; identifying bases included in a base 
sequence to be edited, having location information, and positioned at both 
ends of the base sequence to be edited; and displaying a corresponding 
trace between the identified bases positioned at both ends in 
correspondence with the consensus sequence. 
The fragment trace data display method may additionally include the step of 
displaying the consensus sequence in correspondence with a displayed 
trace, so that an interval between contiguous bases (spaces between 
adjacent bases) in the displayed consensus sequence becomes even 
(regular). 
The fragment trace data display method may further include the steps of: 
providing location information indicating a location on the trace for the 
base included in the fragment base sequence; identifying bases included in 
the fragment base sequence, having the location information, and 
positioned at both ends of the fragment sequence; and displaying a 
corresponding trace between the identified bases at both ends in 
correspondence with the consensus sequence. 
When a type of a base included in the consensus sequence is determined, if 
a type of a base indicated by a base sequence of a first fragment among 
the fragment base sequences is different from that indicated by a base 
sequence of a second fragment among the fragment base sequences, a symbol 
indicating either of the two bases may be used for the base to be 
determined. 
Another method according to the present invention is a method for 
determining a base sequence of a DNA based on base sequences of a 
plurality of fragments forming a portion of the DNA and traces 
representing the base sequences of the plurality of fragments, which are 
obtained by a DNA sequencer. This method includes the steps of: 
determining a consensus sequence by linking the base sequences of the 
plurality of fragments of the DNA obtained by the DNA sequencer; 
determining a base sequence to be edited in the consensus sequence; 
identifying a trace corresponding to the base sequence to be edited among 
traces obtained by the DNA sequencer; and displaying the identified trace 
in correspondence with the base sequence to be edited. 
This method may further include the steps of: providing location data 
indicating a corresponding location on a trace for each of the bases 
included in the base sequences of the plurality of fragments of the DNA; 
identifying the bases included in the base sequence to be edited, having 
the location information, and positioned at both ends of the base sequence 
to be edited; and displaying a trace existing between the location data of 
the identified bases positioned at both ends in correspondence with the 
consensus sequence. 
This method may additionally include the step of displaying the consensus 
sequence in correspondence with the displayed trace, so that an interval 
(spaces) between contiguous bases becomes even (regular). When a type of a 
base included in the consensus sequence is determined, if a type of a base 
indicated by a base sequence of a first fragment among the fragment base 
sequences is different from that indicated by a base sequence of a second 
fragment among the fragment base sequences, a symbol indicating either of 
the two bases may be used for the base. 
A device according to the present invention is intended for determining a 
base sequence of a DNA based on base sequences of a plurality of fragments 
forming a portion of a DNA, and traces representing the base sequences of 
the plurality of fragments, which are obtained by a DNA sequencer. This 
device includes a pre-process unit for determining a consensus sequence by 
linking the base sequences of the plurality of fragments of the DNA 
obtained by the DNA sequencer, an editing data setting unit for 
determining a base sequence to be edited in the consensus sequence, a 
trace data setting unit for identifying a trace corresponding to the base 
sequence to be edited among traces obtained by the DNA sequencer, and a 
trace data display unit for displaying the identified trace in 
correspondence with the base sequence to be edited. 
The pre-process unit may provide location data indicating a corresponding 
location on a trace for each of bases included in the base sequences of 
the plurality of fragments of the DNA, and the edition data setting unit 
may identify bases included in the base sequence to be edited, having the 
location information, and being positioned at both ends of the base 
sequence to be edited. The trace data display unit may display a trace 
existing between location data of the identified bases positioned at both 
ends in correspondence with the consensus sequence. 
The trace data display unit may display the consensus sequence in 
correspondence with a displayed trace, so that an interval (spaces) 
between contiguous bases becomes even (regular). 
When a type of a base included in the consensus sequence is determined, if 
a type of a base indicated by a base sequence of a first fragment among 
the fragment base sequences is different from that indicated by a base 
sequence of a second fragment among the fragment base sequences, a symbol 
indicating either of the two bases may be used for the base. 
A storage medium according to the present invention is intended to store a 
program for making a computer execute the above described method according 
to the present invention. As the storage medium, a floppy disk, any type 
of ROM, a hard disk, a mini disk, or a RAM may be used.

DESCRIPTION OF THE PREFERRED EMBODIMENT 
FIG. 4 is a block diagram showing a fundamental process of a method 
according to the present invention. The method according to the present 
invention is a fragment trace data display method used to determine a base 
sequence of an entire DNA by separating the base sequence of the DNA into 
a plurality of fragments, displaying a trace (waveform) indicating 
locations of bases included in each of the plurality of fragments, and 
linking and editing base sequences corresponding to a plurality of traces. 
With the fragment trace data display method as shown in FIG. 4, a base 
sequence of each fragment is first determined as a fragment base sequence 
in step S1. The fragment base sequence is obtained by, for example, an 
output from a DNA sequencer used for determining a base sequence of a DNA. 
In step S2, fragment base sequences determined in step S1 are linked, so 
that one consensus sequence indicating the base sequence of the entire 
DNA, or a base sequence resulting from linkage of a plurality of 
fragments, is obtained. For the consensus sequence, ambiguity, such as 
indicating that a base at a certain location is either of two bases, 
determining the base sequence using a mark which does not designate a 
particular base, etc., is allowed. 
In step S3, a trace indicating the locations of bases included in each of 
the fragment base sequences is displayed in correspondence with the 
consensus sequence, and an editing operation such as removing an 
unsuitable base, inserting a base depending on need, etc. is performed 
based on a comparison between displayed traces, so that the base sequence 
of the entire DNA with the ambiguity removed is determined. 
With this process, the trace display facilitating the editing operation by 
comparing the displayed traces is performed in correspondence with the 
consensus sequence. The display method is, for example, like the one 
described below. 
Location information indicating a location on a trace is provided to each 
of the bases included in a fragment base sequence output from a DNA 
sequencer. However, such location information is not provided to a base 
inserted into the fragment base sequence during editing. Bases positioned 
at both ends of the fragment base sequence among bases having the location 
information included in the fragment base sequence being edited, are 
identified, so that a corresponding trace is, for example, scale-converted 
and displayed in correspondence with the consensus sequence. 
By performing such a trace data (waveform data) display operation, a 
relationship between a consensus sequence being edited and an original 
trace can be determined with ease, thereby identifying a correct DNA base 
sequence quickly. 
FIG. 5 is a flowchart showing an entire process for linking and editing 
base sequences using the wave display method according to this embodiment. 
The flowchart shown in this figure shows a trace data display process from 
a start, till an update performed each time an event such as linking 
fragments, performing an editing operation, etc. is executed. 
In FIG. 5, an instruction of an event such as linking fragments, performing 
an editing operation, etc. is input in step S11. Then, a pre-process such 
as linking the fragments, rewriting a base sequence, etc. is performed 
depending on need in step S12. Steps S1 and S2 shown in FIG. 4 may be 
included in this step. 
Next, a sequence data link area is updated in step S13. The sequence data 
link area indicates a partial area of a base sequence between bases 
respectively having corresponding trace data closest to the start and the 
end (both ends may be included), among bases in a fragment base sequence 
being edited. 
For a base included in a base sequence obtained as an output from a DNA 
sequencer, its location on trace data, that is, corresponding location 
information, can be known as will be described later. Therefore, such base 
data is stored, for example, in a memory in correspondence with the 
location information. In the meantime, for a base such as the one inserted 
during editing, corresponding location information is not stored. This is 
because a corresponding location on the trace data is unknown. 
Accordingly, the sequence data link area indicates an area between the 
leftmost and rightmost bases respectively, having corresponding location 
information in the fragment base sequence (both ends may be included). 
In FIG. 5, after the sequence data link area is updated and a sequence data 
link area corresponding to the fragment base sequence is obtained in step 
S13, a trace data link area is updated in step S14. The trace data link 
area is an area between locations indicated by trace data location 
information possessed by the bases positioned at both ends of the above 
described sequence data link area, that is, a partial area of trace data 
between locations of the leftmost and rightmost bases. With the update 
process performed in this step, a trace data link area corresponding to 
the sequence data link area in the fragment base sequence to be edited, is 
obtained. 
After the trace data link area corresponding to the sequence data link area 
to be edited is obtained, a trace display is updated (to be described 
later) in step S15. Then, a required post-process and other event 
processes are performed in step S16. In step S17, a main loop process for 
displaying an actual trace is performed. 
Provided next is the explanation about the concept of a consensus sequence 
according to the present invention. To determine a base sequence of a very 
long DNA chain as described above, the DNA is separated into a plurality 
of fragments. After a base sequence in each of the plurality of fragments 
is determined using a DNA sequencer, the base sequence of the entire DNA 
is determined by linking and editing the base sequences of the plurality 
of fragments. One base sequence produced in a process for linking base 
sequences of a plurality of fragments in order to determine a base 
sequence of an entire DNA, is called a consensus sequence. An example of 
the consensus sequence is provided below. Note that this example shows 
only one of the double chains. 
______________________________________ 
base number 1 5 10 15 20 25 
consensus sequence 
ATGCTTAGSWGTACCARGGTAAAAA 
fragment A ATGCTTAGCTGTACCAG 
fragment B TTAGGT-TACCAAGGTA 
fragment C AGCAGTACCAAGGTAAAAA 
______________________________________ 
This example shows a consensus sequence generated by linking three 
fragments A, B, and C. If overlapped bases are identical in overlapped 
portions of the fragments, they are used as bases in the consensus 
sequence as they are. If the overlapped bases are different, they are 
represented by an IU code. That is, if a base in the overlapped 
portions is considered to be either of C and G, it is replaced with "S" 
(corresponding to the above described base number 9). If the base is 
considered to be either of T and A, it is replaced with "W" (corresponding 
to the base number 10). If the base is considered to be either of G and A, 
it is replaced with "R" (corresponding to the base number 17). By 
performing these replacements, the consensus sequence is obtained. 
Provided next is the explanation about a structure of the data used for the 
trace data display method according to the present invention. As the data 
used by the trace data display method according to the present invention, 
consensus data set for each consensus sequence can be generated. The 
consensus data includes "Fragment Cnt" indicating a fragment number (the 
number of fragments) belonging to the consensus sequence, a pointer 
"pFragment Fragment Cnt!" pointing to information specific to a fragment 
belonging to the consensus sequence (to be described later), and a 
"Consensus Consensus Cnt!" indicating a base sequence of the consensus 
sequence. 
Provided next is the explanation about fragment data used by the trace data 
display method. The fragment data includes trace data, original base 
sequence data, base sequence data for editing, base data for editing, and 
fragment-specific information. 
The trace data includes trace data of each of the four bases, that is, 
adenine A, thymine T, guanine G, and cytosine C. Data obtained by 
performing approximately 10,000 samplings at predetermined intervals, is 
stored as each trace data of each of the bases. At this time, the trace 
data has a two-dimensional sequence. That is, at 10,000 data points 
represented by a data point location "x", data such as 16-bit data 
indicating a height of each trace is stored. Here, each trace data is 
represented as follows: 
WaveData 0! x!: trace data of A (adenine) 
WaveData 1! x!: trace data of T (thymine) 
WaveData 2! x!: trace data of G (guanine) 
WaveData 3! x!: trace data of C (cytosine) 
x: data point location (wave data point) 
The original base sequence data, which is obtained by a DNA sequencer, is a 
fragment base sequence before linking or editing. An example of the 
original base sequence data is provided in FIG. 7. As shown in this 
figure, the original base sequence data is represented by associating each 
of the bases included in an original fragment and its location with a base 
number "n" (the original base number "OriginalBaseNumber"). A base type is 
represented by a base code (BC) conforming to the IU code, while a base 
location is represented by a wave data point, that is, the data point 
location "x" (data point location at a peak of a trace corresponding to 
each of the bases) shown in FIG. 6. 
The original base sequence data is represented by an original base having 
the following symbol. 
Originalbase n-1!: original base (n: base number, 1.ltoreq.n.ltoreq.total 
number of original base sequences!) 
The base sequence data for editing is data representing a base sequence to 
be edited, composed of a number of a base being edited (m) and a pointer 
(P) pointing to base data for editing, to be described next. The base 
sequence data for editing is represented by an edit base having the 
following symbol. 
pEditBase m-1!: edit base (m: base number being edited, 
1.ltoreq.m.ltoreq.total number of bases in a base sequence being edited! 
The base data for editing is data pointed to by a pointer of the base 
sequence data for editing, and includes a base code (BC) and an original 
base number "OriginalBaseNumber". The base code (BC) is a character 
indicating a base type, while the original base number 
"OriginalBaseNumber" is a number of a base "n" in an original base 
sequence indicated by the base code (BC). For a base which does not have a 
corresponding base in an original base sequence, such as the one inserted 
during editing, the original base number is defined as "-1". 
FIG. 8 shows both the base sequence data for editing and the base data for 
editing. The base sequence data for editing is a sequence of the pointer P 
pointing to base data for editing in correspondence with a base number, as 
described above. Since a base in a structure "T" pointed to by a pointer 
P.sub.3 does not exist in original base sequence data which is the second 
data, the original base number of this base is 
The fragment-specific information is information specific to each fragment 
corresponding to trace data and sequence data. The fragment-specific 
information includes the following data. 
pwave: pointer pointing to WaveData 
pOriginalData: pointer pointing to OriginalBase 
pEditData: pointer pointing to pEditBase 
OffsetBase: first location of a fragment in a consensus sequence (offset 
base) 
LeftBaseNumber: base number at a left end of sequence data link area in a 
base sequence for editing 
RightBaseNumber: base number at a right end of a sequence data link area in 
trace data 
LeftWaveDataPoint: location of a data point at left end of trace data link 
area in trace data 
RightWaveDataPoint: location of a data point at right end of trace data 
link area in trace data 
The offset base "OffsetBase" indicates where the beginning (left end) of a 
base sequence of each fragment is positioned in a consensus sequence. In 
the above described example of the consensus sequence, the offset base of 
the fragment B is 5. 
Provided next is the detailed explanation about a process performed in 
steps S13 through S15 according to this embodiment, by referring to FIGS. 
9 through 11. 
FIG. 9 is a flowchart showing a process for updating a sequence data link 
area performed in step S13. In this figure, for all of the edit bases 
(pEditBases), that is, all of the bases included in the base sequence data 
for editing, the original base number "OriginalBaseNumber", which is a 
number of the base data for editing, is examined (step S21). A base whose 
original base number "OriginalBaseNumber" is not "-1" is identified (step 
S22). Base numbers of the leftmost and rightmost bases among identified 
bases are stored as a left base number "LeftBaseNumber" and a right base 
number "RightBaseNumber" respectively (steps S23 and 24). 
FIG. 10 is a flowchart showing the process performed in step S14 of FIG. 5, 
that is, the process for updating a trace data link area. As shown in this 
figure, a location of an original base corresponding to the left base 
number "LeftBaseNumber" obtained in FIG. 9, that is, a wave data point "x" 
corresponding to a base number "n" of the same base in the original base 
sequence data, is obtained (step S31). The obtained wave data point is 
stored as the left wave data point "LeftWaveDataPoint") (step S32). 
Similarly, a location of an original base "x" corresponding to the right 
base number "RightBaseNumber" is obtained (step S33). A wave data point 
"WaveDataPoint" in the original base sequence data corresponding to the 
right base number "RightBaseNumber", is stored as a right wave data point 
"RightWaveDataPoint". (step S34). 
FIG. 11 is a flowchart showing the process performed in step S15 of FIG. 5, 
that is, the process for updating a trace display. In this step, scale 
conversion is performed for four sets of trace data "WaveData" 
respectively corresponding to the four bases, so that a trace between the 
left wave data point "LeftWaveDataPoint" and the right wave data point 
"RightWaveDataPoint" corresponds to a portion between the left base number 
"LeftBaseNumber" and the right base number "RightBaseNumber", in a 
consensus sequence, when displayed (step S41). The trace after the scale 
conversion is then displayed (step S42). 
That is, according to the present invention, a trace corresponding to each 
fragment is scale-converted and displayed at a location corresponding to a 
consensus sequence. Each time any change is made to a location of a base 
in a fragment base sequence or its contents due to a process such as an 
editing process, etc., the location of the trace data is scale-converted 
and displayed. 
Assume that the number of bases included in a fragment base sequence is 
changed from 345 to 350 due to an editing process, etc., and this fragment 
base sequence ranges from a 101st base to a 450th base in a consensus 
sequence. In this case, the scale conversion and a shift of display 
location, etc. are performed, so that the first base of the fragment base 
sequence is moved to the 101st location, and the 350th base originally 
positioned at the 345th location is moved to the 450th location. Then, a 
trace after editing is displayed. That is, when the number of bases is 
changed to "n+5" by an operation such as a linking operation or an editing 
operation for a fragment whose number of bases is determined to be "n" by 
a DNA sequencer, a trace corresponding to the sequence composed of "n" 
bases determined by the DNA sequencer is displayed in a range of "n+5" 
bases. 
According to the present invention, a distortion correction for 
automatically correcting the distortion of a distance travelled by a gel 
electrophoresis is made to equalize base intervals corresponding to a 
trace, thereby facilitating a simple comparison between traces. The method 
for making the distortion correction is described below. 
When a molecule with a molecular weight equal to or less than 300,000 is 
electrophoresed in a gel, it is experimentally proved that the following 
equation between the travelling speed of the molecule and the molecular 
weight is approximately satisfied. 
EQU v=-C.sub.1 .multidot.log m+C.sub.2 (1) 
(m: molecular weight&gt;0, v: moving speed&gt;0, C.sub.1 : constant&gt;0, C.sub.2 : 
constant&gt;0) 
The measurement of fluorescence intensity is performed at predetermined 
intervals (T.sub.1 &gt;0) set for each experiment. Assuming that a 
predetermined distance between a location at which the electrophoresis 
starts and a location at which the fluorescence intensity is detected, is 
C.sub.3 &gt;0 
EQU C.sub.3 =v (T.sub.1 x+T.sub.2) (2) 
(x=the number of data points from the first detected base) 
(T.sub.2 : the amount of time from the electrophoresis start till the 
detection of the first (x=0) base&gt;0) 
This embodiment is based on the assumption that the trace display data does 
not include data immediately after the start of electrophoresis. That is, 
data of the fluorescence intensity starts to be captured after a 
predetermined amount of time elapses from the start of electrophoresis. To 
take advantage of the equation (1), a distance between the location at 
which the electrophoresis starts, that is, the location at which a sample 
is injected, to the location at which the fluorescence intensity is 
detected, must be obtained. This distance is represented by the equation 
(2). T.sub.2 in the equation (2) is an amount of time from the start of 
electrophoresis, that is, a time point at which a voltage is applied, till 
a time point at which the fluorescence intensity starts to be captured as 
data. The data of the fluorescence intensity is measured at predetermined 
intervals (T.sub.1)--normally at one-second intervals, and "x" indicates 
the number of data points. "v" in the equation (2) indicates an 
electrophoresis speed of a DNA base measured as "xth" data. Note that the 
start of electrophoresis means a time point at which a voltage is applied 
to an electrophoresis device, and the fluorescent intensity is measured 
from the time point at which the electrophoresis starts, but its data is 
started to be kept after a predetermined amount of time elapses. 
By using the equations (1) and (2), an equation for associating the number 
of data points "x" whose base intervals are corrected to be even (regular) 
with the base number "n", is defined as follows. 
First of all, from both of the equations (1) and (2) 
EQU C.sub.3 /(T.sub.1 x+T.sub.2)=-C.sub.1 log m+C.sub.2 log m=-C.sub.3 /C.sub.1 
(T.sub.1 x+T.sub.2)+C.sub.2 /C.sub.1 (3) 
Assuming 
C.sub.4 =C.sub.3 /C.sub.1 &gt;0, C.sub.5 =C.sub.2 /C.sub.1 &gt;0 
the equation (3) is therefore, 
EQU log m=-C.sub.4 /(T.sub.1 x+T.sub.2)+C.sub.5 (4) 
Also assuming that a molecular weight of a primer is M.sub.P, the base 
number is n, and an average molecular weight of bases is M.sub.B, 
EQU m=M.sub.P +(n-1) M.sub.B (5) 
can be obtained. 
If the equation (5) is assigned to the equation (4), 
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log {M.sup.P + (n - 1) M.sub.B } = --C.sub.4 /(T.sub.1 x + T.sub.2) + 
C.sub.5 
M.sub.P + (n- 1) M.sub.B = 10 .sup.- {--C.sub.4 /T.sub.1 x + T.sub.2) + 
C.sub.5 } 
.thrfore. n = f (x) 
= 10 .sup.- {--C.sub.4 /(T.sub.1 x + T.sub.2) + C.sub.5 } - M.sub.P 
!/M.sub.B + 1 
. . . (6) 
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where M.sub.P is defined as a molecular weight of a primer for each 
sequencing. 
For M.sub.B, an average molecular weight of bases 316 is used. As T.sub.1, 
a measurement interval set in sequencing is used. As T.sub.2, an amount of 
time from the start of electrophoresis till the detection of the first 
(n=0) base is used. 
For a trace display, the constants C.sub.4 and C.sub.5 in the equation (6) 
are determined from the corresponding actual electrophoresis data to be 
used. 
For this determination, RightBaseNumber and LeftBaseNumber are used. That 
is, if n=RightBaseNumber, x=xRightBaseNumber!. Or, if n=LeftBaseNumber, 
x=xLeftBaseNumber!. Therefore, by assigning these equations to the 
equation (6), the constants C.sub.4 and C.sub.5 are determined for each 
fragment. 
Normally, "x" is defined as a horizontal axis for a trace display, but here 
"n" is defined as the horizontal axis. The scale conversion is performed 
by using trace data corresponding to "n", which ranges from LeftBaseNumber 
to RightBaseNumber, and its result is displayed. 
As described above, a sequence of trace data whose base intervals are 
corrected to be approximately regular, is obtained based on the equation 
(6). Its result is stored, for example, in a memory, and used for 
displaying a trace. The data shown in FIGS. 6 and 7 are updated according 
to the result of this calculation, while the data shown in FIG. 8 is not 
updated. 
FIGS. 12 and 13 are schematic diagrams showing a fragment trace display 
varying due to the above described editing process. FIG. 12 shows an 
output from a DNA sequencer as it is, while FIG. 13 shows a result of 
using the trace data display method according to the present invention. It 
is understood from the figure that the base intervals of the lowest traces 
are regular in comparison with the upper traces. 
The above described method according to the present invention can be 
implemented, for example, by a control device employing a computer. As 
shown in FIG. 14, the control device comprises a processing device 10, a 
storing device 20, a display device 30, an input unit 40, and a data read 
device 50. 
The processing device 10 comprises a pre-process unit 12 for performing the 
pre-process in step S12 of FIG. 5, an editing data setting unit 13 for 
performing the process for updating a sequence data link area in step S13, 
a trace data setting unit 14 for performing the process for updating a 
trace data link area in step S14, a trace data display unit 15 for 
performing the process for updating a trace display in step S15, a 
post-event process unit 16 for performing a post-process and other event 
processes in step S16, and a main loop process unit 17 for performing the 
main loop process in step S17. Note that the processing device 10 may 
include any of the units for performing processes in respective steps of 
FIGS. 4, 5, and 9 through 11 among the steps of the method according to 
this embodiment. 
The storing device 20 stores a program used for performing the above 
described processes, data used for each of the processes, and data created 
or updated by each of the processes. A hard disk, a RAM, a ROM, or an 
information storing unit of various types, may be employed as the storing 
device 20. These program and data may be stored in an external storage 
medium. They may be input/output to/from the processing device 10 via the 
data read device 50. A magnetic disk, an optical disk, a magneto-optical 
disk, and other storage media may be employed as the external storage 
medium. 
The display device 30 is used to display a graph representing a base 
sequence and a base trace in the processes of the present invention as 
shown in FIGS. 12 and 13. The display unit 30 is also used to display a 
menu for selecting a program used for executing the method according to 
the present invention, and to select data of various types. A user may 
select the program and the data of various types via the input unit 40. 
FIG. 15 is a schematic diagram showing a computer system for implementing 
the present invention. By programming the method according to the present 
invention, and making the computer system execute the method, the system 
can be used as a processing device according to the present invention. 
This computer system comprises a computer 100, a display device 110, and an 
input device 120. The computer 100 comprises a processing device 101, a 
memory 102, and a driver for a storage medium 103. The input device 
comprises a keyboard and a mouse. 
The processing device 101, which corresponds to the processing device 10 
shown in FIG. 14, performs each of the programmed processes in this 
embodiment. The memory 102, which corresponds to the storing device 20 
shown in FIG. 14, stores a program for performing each of the processes, 
data used for each of the processes, and data and files required for other 
processes. The processes according to the present invention may be 
programmed and stored in a storage medium. The driver 103 is intended to 
read a program stored in such a storage medium, and corresponds to the 
data read device 50 shown in FIG. 14. An optical medium, a magnetic 
medium, and a magneto-optical medium such as a floppy disk, a CD-ROM, an 
MD, etc. may be employed as the storage medium. 
The display device 110, which corresponds to the display device 30 shown in 
FIG. 14, displays a graph created during, or as a result of, a process of 
the present invention. The input device 120 is used by a user in order to 
give instructions for performing a process of the present invention to a 
computer system. 
According to the present invention as described above in detail, a trace 
can be displayed, compared and studied in real time in correspondence with 
a linkage or editing state of fragments, for example, simultaneously with 
an editing operation. As a result, a base sequence can be determined while 
visually verifying the accuracy of a result of linkage or editing process. 
Additionally, since the linkage and the editing can be performed while 
verifying the consistency of the trace data, as well as the consistency in 
a character sequence as a base symbol sequence, the base sequence can be 
assembled more accurately and more quickly. Furthermore, base intervals 
corresponding to traces can be made even, thereby facilitating a 
comparison between traces. As a result, sequencing mistakes can be 
prevented. 
__________________________________________________________________________ 
SEQUENCE LISTING 
(1) GENERAL INFORMATION: 
(iii) NUMBER OF SEQUENCES: 1 
(2) INFORMATION FOR SEQ ID NO:1: 
(i) SEQUENCE CHARACTERISTICS: 
(A) LENGTH: 15 base pairs 
(B) TYPE: nucleic acid 
(C) STRANDEDNESS: double 
(D) TOPOLOGY: linear 
(ii) MOLECULE TYPE: DNA (genomic) 
(iii) HYPOTHETICAL: NO 
(iv) ANTI-SENSE: NO 
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: 
CCATAAATAACCTTT15 
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