CN102708308A - Method for realizing visualization of DNA (deoxyribonucleic acid) sequences - Google Patents
Method for realizing visualization of DNA (deoxyribonucleic acid) sequences Download PDFInfo
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- CN102708308A CN102708308A CN2012100950289A CN201210095028A CN102708308A CN 102708308 A CN102708308 A CN 102708308A CN 2012100950289 A CN2012100950289 A CN 2012100950289A CN 201210095028 A CN201210095028 A CN 201210095028A CN 102708308 A CN102708308 A CN 102708308A
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- dna sequence
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Abstract
The invention provides an improved model for realizing the visualization of the spectrum of a two-dimensional space by improving a spectral model. The improved model is used for a string of DNA (deoxyribonucleic acid) sequences and is characterized by being capable of avoiding the loss of information, being clear and intuitive and being convenient for comparing a plurality of DNA sequences. The graph for realizing the visualization of the DNA sequences is drawn by a computer, comprises a line A, a line B, a line C and a line D which are parallel one another and is used for displaying the four lines periodically. The lines in the graph are marked according to the appearance sequence of the DNA sequences by adopting the jump rule and the marking points are connected to form a line graph, therefore, the visualization of the DNA sequences is realized.
Description
Technical field
The present invention relates to a kind of visable representation method of gene order, belong to field of bioinformatics.
Background technology
Dna sequence dna is by A (adenine), T (thymine), and G (guanine), four nucleotide of C (cytimidine) are formed.The DNA data can be with the stores of character in computer.Though this mode is convenient to preserve, but be not easy to people's observation.Therefore develop a kind of aid and help observation and analyzing DNA data and therefrom excavate valuable information, have important and practical meanings.
Since first dna sequence dna Visualization Model proposed, the dna sequence dna visualization technique was flourish, and a large amount of scholars have made great efforts and contribution; But in same model, solve following five problems simultaneously is quite difficult; Be respectively: the information dropout problem, at the problem that higher dimensional space is difficult to observe, degenerate problem; The problem that the length dna sequence is difficult to observe at two-dimensional space, the problem of needs reflection useful information.Therefore,, realize visual inspection and analyzing DNA data, demand development of new dna sequence dna method for visualizing urgently for overcoming the above problems.
Summary of the invention
?[0006]
The object of the invention: the present invention is the visual spectral model of a kind of improved dna sequence dna, and this model is A, G; T; Four parallel lines periodizations of C show, the order that occurs according to dna sequence dna through the redirect rule successively in the drawings mark connect into broken line graph, realize the visual of dna sequence dna.The method that the present invention proposes can solve the degenerate problem of original dna sequence dna Visualization Model, the problem that problem that information dropout problem, length dna sequence are difficult to observe in two-dimensional space and needs reflect useful information.
Technical scheme of the present invention:
1) A, G, T, the C parallel lines: equidistant 4 parallel lines that draw, with A, G, T, four parallel lines of the sequence notation of C.
2) A, G, T, the periodization of C parallel lines: duplicate four parallel lines, and the Y direction in plane space is expanded.
3) redirect rule: this rule comprises two parts: 1, when the nucleotide quantity of section of DNA sequence more than or equal to 10 the time, just carrying out or negative redirect according to the information of last nucleotide of this section sequence; 2, comprised complete A when one section sequence, G, T during C nucleotide information, is just carrying out or negative redirect (if when ending nucleotide is A, is then jumped one-period to Y axle negative direction according to the information of last nucleotide of this section sequence; If when ending nucleotide is G, then jump two cycles to Y axle negative direction; If when ending nucleotide is T, then jump one-period to Y axle positive dirction; If when ending nucleotide is C, then jump two cycles) to Y axle positive dirction.
The present invention compared with prior art has following beneficial effect:
Former spectrogram model is the two-dimensional visualization model, and can solve degenerate problem and data loss problem simultaneously.But when dna sequence dna length was longer, the effect of visualization of former spectral model will variation.And the present invention has on the advantage basis of former spectral model; Also overcome the shortcoming of former spectral model: degenerating and the information dropout problem not only can not appear in the present invention; No matter dna sequence dna is long or short; Can both in two-dimensional space, present graphical effect preferably, and the length of reflection dna sequence dna.
Description of drawings
With reference to figure below, through by way of example the present invention is described, wherein:
Fig. 1 is the initial light spectrogram, wherein, A, G, T, four equidistant drawing of parallel lines of C, and mark comes out;
Fig. 2 is the periodization spectrogram, wherein, and A, G, T, C parallel lines periodization figure;
Fig. 3 is according to the nucleotide sequence in the dna sequence dna, does marked according on the parallel lines of redirect rule in Fig. 2;
Fig. 4 is on the basis of Fig. 3, connects adjacent point with straight line, and gets presentation graphs to the end.
Embodiment
The visual broken line graph of setting up dna sequence dna that is meant of dna sequence dna, promptly the form with figure shows dna sequence dna, thereby avoids character string, reaches the purpose of analyzing and understanding dna sequence dna through observing picture, helps people to excavate the valuable information of dna sequence dna.
Utilize MATLAB to carry out method of the present invention.The embodiment of dna sequence dna method for visualizing of the present invention is described referring to figs. 1 through Fig. 4.
With reference to Fig. 1, at first equidistant four parallel lines that draw, and with A, G, T, four parallel lines of the sequence notation of C.First is nucleotide A (adenine), and mark article one parallel lines are A.Second is G (guanine), and mark second parallel lines are G, by that analogy.
With reference to Fig. 2, with A, G, T, four parallel lines periodizations of C show.
3, (be among Fig. 3 dna sequence dna be " ATGGTGCATCGAAGGC ") according to given dna sequence dna and according to redirect rule, makes marks in Fig. 2.By shown in Figure 3, first nucleotide is A, on the A of first position line, makes marks.Second nucleotide is T, on the T of second position line, makes marks.By that analogy, perhaps work as dna sequence dna up to the number of this section nucleotide more than or equal to 10 and comprise complete A, G, redirect during C nucleotide information, according to the information of last nucleotide in this section, takes place in T.For example, just in time comprised complete A in preceding 7 the nucleotide information " ATGGTGC " in this segment DNA sequence, G, T, C information is simultaneously because the nucleotide information of " ATGGTGC " ending place is C.Therefore, according to redirect rule, dna sequence dna afterwards (" ATCGAAGGC ") will be from current location the A parallel lines beginning label along two cycles of Y axle positive dirction, and by that analogy.
With reference to Fig. 4, couple together adjacent point with straight line, get presentation graphs to the end.Therefore here first point is A, and second point is T, between A and T, is connected with straight line.The 3rd point is G, therefore T is connected with G, by that analogy.
Claims (10)
1. dna sequence dna visualization method, said method comprises:
Equidistant four parallel lines that draw.
2. duplicate A, G, T, four parallel lines of C make its periodization.
3. according to the nucleotide sequence in the dna sequence dna, on the respective parallel line, make marks according to the redirect rule.
4. connect adjacent point with straight line and obtain the dna sequence dna presentation graphs.
5. method for visualizing as claimed in claim 1, wherein, four parallel lines are pressed A, G, T, the order of C marks.
6. method for visualizing as claimed in claim 1 wherein, duplicates four parallel lines, and the Y direction in plane space expands, and makes its periodization.
7. method for visualizing as claimed in claim 1, wherein, the redirect rule be when the nucleotide quantity of section of DNA sequence more than or equal to 10 the time, just carrying out or negative redirect according to the information of last nucleotide of this section sequence.
8. perhaps work as one section sequence and comprised complete A, G, T during C nucleotide information, is just carrying out or negative redirect according to the information of last nucleotide of this section sequence.
9. method for visualizing as claimed in claim 4, wherein, just perhaps negative redirect is meant as if end up when nucleotide is A, then jumps one-period to Y axle negative direction; If when ending nucleotide is G, then jump two cycles to Y axle negative direction; If when ending nucleotide is T, then jump one-period to Y axle positive dirction; If when ending nucleotide is C, then jump two cycles to Y axle positive dirction.
10. the present invention is a kind of computer program, and it is included in when moving on the suitable computing machine, is adapted for the computer program code of the method for enforcement of rights requirement 1.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN2012100950289A CN102708308A (en) | 2012-03-31 | 2012-03-31 | Method for realizing visualization of DNA (deoxyribonucleic acid) sequences |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
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| CN2012100950289A CN102708308A (en) | 2012-03-31 | 2012-03-31 | Method for realizing visualization of DNA (deoxyribonucleic acid) sequences |
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| CN102708308A true CN102708308A (en) | 2012-10-03 |
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| CN2012100950289A Pending CN102708308A (en) | 2012-03-31 | 2012-03-31 | Method for realizing visualization of DNA (deoxyribonucleic acid) sequences |
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Citations (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1584027A (en) * | 2004-06-10 | 2005-02-23 | 上海交通大学 | RNA sequential characteristic visual extracting method |
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2012
- 2012-03-31 CN CN2012100950289A patent/CN102708308A/en active Pending
Patent Citations (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1584027A (en) * | 2004-06-10 | 2005-02-23 | 上海交通大学 | RNA sequential characteristic visual extracting method |
Non-Patent Citations (2)
| Title |
|---|
| STEPHEN S. -T. YAU等: "DNA sequence representation without degeneracy"", 《NUCLEIC ACIDS RESEARCH》 * |
| 张柱金: "DNA序列二维可视化研究", 《中国博士学位论文全文数据库》 * |
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Application publication date: 20121003 |