Electrophoretic trace simulator
View Patent ↗A simulated electrophoretic trace is prepared by first obtaining an input file containing an input base sequence comprising a string of letters (A, C, G and/or T) in an order corresponding to the input base sequence, and then modifying the input file using one or more functions to take into account perturbations associated with (1) changes in peak intensity as a function of base number; (2) peak shape as a function of base number; (3) peak skew; (4) spacing between peaks; (5) background; (6) noise; (7) spectral cross-talk; (8) instrumental effects and/or (9) gel electrophoresis effects to produce a modified file representing a simulated electrophoretic trace. The method may be performed using a specially adapted apparatus.
1. A method for creating a simulated electrophoretic trace for use in sequencing a sample polynucleotide sequence, comprising the steps of
(a) obtaining an input file containing an input base sequence, derived from an expected reference base sequence independent of the sample polynucleotide sequence, comprising a string of letters (A, C, G and/or T) in an order corresponding to the input base sequence;
(b) modifying the input file using one or more functions to introduce distortions associated with (1) changes in peak intensity as a function of base number; (2) peak shape as a function of base number; (3) peak skew; (4) spacing between peaks; (5) background; (6) noise; (7) spectral cross-talk; (8) instrumental effects and/or (9) gel electrophoresis effects to produce a modified file representing a simulated electrophoretic trace.
2. The method of claim 1 , wherein the input file is a text file.
3. The method of claim 1 , wherein the input file is an experimentally recorded data trace recorded from an automated DNA sequencer.
4. The method of claim 1 , wherein peak intensity in the simulated electrophoretic trace is modified as a function of base number in accordance with the function
I i ( N ) =I oi exp(−β i N )
where i=type of base (A, C, G, T), N=base number, I i (N)=intensity of ladder of type i as function of base number, I 0i =intensity of unextended primer within ladder of type i, and β i =exponential decay parameter for the intensity of ladder of type i.
5. The method of claim 1 , wherein peak shape in the simulated electrophoretic trace is modified as function of base number in accordance with the function
I
N
(
t
)
=
I
N0
σ
N
2
π
exp
(
-
(
t
-
t
N
)
2
2
(
σ
N
)
2
)
where I N (t)=fluorescent intensity at time t, within the peak corresponding to base number N; I N0 =intensity maximum of this peak, σ N =width of peak (Gaussian standard deviation), and t N =center of the peak.
6. The method of claim 1 , wherein spacing between peaks in the simulated electrophoretic trace is modified as a function of base number in accordance with the function
t
(
N
)
=
t
0
+
∑
i
a
i
N
i
(
4
)
where a i are the polynomial coefficients, and i is the degree of the polynomial.
7. An apparatus for generating a simulated electrophoretic trace comprising a programmed computer processor connected for communication with a storage device having stored thereon a set of program instructions for carrying out the method of any of claims 1 – 6 .
8. A method for determining the nucleotide sequence of a sample polynucleotide, comprising the steps of
(a) generating a simulated base sequence by (i) obtaining an input file containing an input base sequence derived from an expected reference base sequence independent of the sample nucleotide sequence, comprising a string of letters (A, C, G and/or T) in an order corresponding to the input base sequence, and (ii) modifying the input file using one or more functions to introduce distortions associated with (1) changes in peak intensity as a function of base number, (2) peak shape as a function of base number, (3) peak skew, (4) spacing between peaks, (5) background, (6) noise, (7) spectral cross-talk, (8) instrumental effects, and/or (9) gel electrophoresis effects, to produce a modified file representing a simulated electrophoretic trace;
(b) obtaining an experimental base sequence of a sample;
(c) comparing the experimental base sequence of the sample with the simulated base sequence; and
(d) correlating bases of the experimental base sequence with corresponding bases of the simulated base sequence, to thereby determine the sequence of the sample.