Primer designing method, apparatus, and device

Abstract

The present invention provides a primer designing method, an apparatus, and a device. The primer designing method comprises: acquiring a double-stranded structure of a target base sequence; acquiring, from a single strand of the double-stranded structure, a primer to be determined; modifying said primer and determining in real time whether a primer parameter in a prompt interface of said primer satisfies a preset condition; and when the primer parameter satisfies the preset condition, using said corresponding primer as a determined target primer. The present invention can quickly complete primer design, thereby improving the efficiency of the primer design; and a user can complete the primer design by means of a mouse dragging operation without complex operations, such that users who are unfamiliar with primer design software can also complete the primer design, thereby improving user experience.

Description

A primer design method, device and equipment TECHNICAL FIELD

[0001] The present application relates to the technical field of biomolecules, in particular to a primer design method, device and equipment. BACKGROUND

[0002] The purpose of primer design is to find a pair of suitable nucleotide fragments that can effectively amplify the template DNA or RNA sequence. At present, primers are mainly designed by biomolecular design software. However, in the prior art, the user needs to be very familiar or proficient in various functions of the molecular design software, and then through very complex operations, the primer can be designed, which is very inconvenient for primer design, the efficiency of primer design is very low, and the user experience is seriously reduced. SUMMARY

[0003] The present application provides a primer design method, device and equipment to solve the problem of low efficiency and low user experience in the prior art.

[0004] A primer design method, comprising:

[0005] Obtaining a double-stranded structure of a target base sequence;

[0006] Obtaining a tentative primer from one single strand of the double-stranded structure;

[0007] Modifying the tentative primer and determining in real time whether the primer parameters in the prompt interface of the tentative primer meet the preset conditions;

[0008] When the primer parameters meet the preset conditions, the corresponding tentative primer is taken as a determined target primer.

[0009] Preferably, obtaining a tentative primer from one single strand of the double-stranded structure comprises:

[0010] Selecting a continuous base sequence as a tentative primer from one single strand of the double-stranded structure by marquee, single selection, or a common way of marquee and single selection.

[0011] Preferably, the modification of the tentative primer comprises:

[0012] Moving the horizontal position of the tentative primer on the single strand; and / or

[0013] Changing the number of bases in the tentative primer;

[0014] The changing of the number of bases in the tentative primer comprises moving the 5' end or / and 3' end of the tentative primer to increase or decrease the number of bases in the tentative primer.

[0015] Preferably, the display screen displays the name of the pending primer or / and a primer figure defining the pending primer, and the moving the horizontal position of the pending primer on the single strand comprises:

[0016] dragging the name of the pending primer to move the horizontal position of the pending primer on the single strand; or / and

[0017] dragging the primer figure or placing the mouse pointer inside the primer figure to move the horizontal position of the pending primer on the single strand.

[0018] Preferably, the primer figure is a frame enclosing the pending primer.

[0019] Preferably, the display screen displays a primer figure defining the pending primer, and the moving the 5' end or / and 3' end of the pending primer comprises:

[0020] moving the two ends of the pending primer defined by the primer figure to move the 5' end or / and 3' end of the pending primer.

[0021] The primer figure is any one or a combination of any two or more of a rectangle, an irregular rectangle, and a boundary line composed of lines.

[0022] Preferably, the primer design method further comprises:

[0023] displaying a prompt interface of the pending primer on the display screen;

[0024] The displaying the prompt interface of the pending primer on the display screen comprises: triggering the displaying of the prompt interface of the pending primer on the display screen when the mouse pointer hovers over the name of the pending primer or the pending primer itself; and

[0025] When the pending primer is being modified, the prompt interface of the pending primer is triggered to be displayed on the display screen, and the prompt interface is in a real-time display state.

[0026] Preferably, the modifying the pending primer and determining in real time whether the primer parameters in the prompt interface of the pending primer meet the preset conditions comprises:

[0027] moving the horizontal position of the pending primer on the single strand and determining in real time whether the primer parameters in the prompt interface of the pending primer meet the preset conditions.

[0028] The primer design method further comprises:

[0029] when none of the primer parameters meet the preset condition, based on the target length of the pending primer and the start and end positions on the single strand corresponding to the pending primer, respectively extending N target length base sequences before and after the start and end positions, N being an integer greater than or equal to 1;

[0030] screening, from the 2N target length base sequences, base sequences corresponding to primer parameters meeting the preset condition and having no overlapping sites with the double-stranded structure to form a first set;

[0031] selecting one of the base sequences in the first set and moving the pending primer horizontally to the selected base sequence to form a target primer.

[0032] Preferably, after the N target length base sequences are respectively extended before and after the start and end positions, the primer design method further comprises:

[0033] screening, from the 2N target length base sequences, base sequences corresponding to primer parameters meeting the preset condition and having no overlapping sites with the corresponding single-stranded structure to form a second set;

[0034] when the first set is empty, selecting one of the base sequences in the second set and moving the pending primer horizontally to the selected base sequence to form a target primer.

[0035] Preferably, when the N target length base sequences are respectively extended before and after the start and end positions, if the base sequences in the corresponding direction are insufficient to obtain the N target length base sequences, the actual number obtained is used.

[0036] Preferably, the pending primer is modified and it is determined in real time whether the primer parameters in the prompt interface of the pending primer meet the preset condition, comprising:

[0037] changing the number of bases in the pending primer and determining in real time whether the primer parameters in the prompt interface of the pending primer meet the preset condition;

[0038] The primer design method further comprises:

[0039] when none of the primer parameters meet the preset condition, based on the target position on the single strand corresponding to the 3' end of the pending primer, sequentially extending P to Q bases in the direction opposite to the primer direction of the pending primer from the target position to form Q-P+1 base sequences, P and Q being integers greater than or equal to 1, and Q being greater than P;

[0040] screening, from the Q-P+1 base sequences, base sequences corresponding to primer parameters meeting the preset condition and having no overlapping sites with the single strand corresponding to the pending primer as a third set;

[0041] selecting, from the third set, a base sequence with the shortest length as a corresponding target primer;

[0042] Preferably, the P is greater than or equal to 10, and the Q is less than or equal to 99.

[0043] Preferably, the primer parameters include one or more of an annealing temperature, a GC content, a number of overlapping sites, and a number of binding sites.

[0044] A primer design device, comprising:

[0045] a structure acquisition module configured to acquire a double-stranded structure of a target base sequence;

[0046] a primer acquisition module configured to acquire a tentative primer from one single strand of the double-stranded structure;

[0047] a modification and determination module configured to modify the tentative primer and determine, in real time, whether primer parameters in a prompt interface of the tentative primer meet preset conditions;

[0048] a target module configured to, when the primer parameters meet the preset conditions, take a corresponding tentative primer as a determined target primer.

[0049] Preferably, the primer acquisition module is specifically configured to select a continuous base sequence as a tentative primer from one single strand of the double-stranded structure by means of a box selection, a single selection, or a box selection and a single selection.

[0050] Preferably, the modification and determination module is specifically configured to:

[0051] move a horizontal position of the tentative primer on the single strand; and / or

[0052] change a number of bases in the tentative primer;

[0053] The changing of the number of bases in the tentative primer includes moving a 5' end or / and a 3' end of the tentative primer to increase or decrease the number of bases in the tentative primer.

[0054] Preferably, a name of the tentative primer or / and a primer graphic defining the tentative primer is displayed on a display screen, and the modification and determination module is further configured to:

[0055] drag the name of the tentative primer to move the horizontal position of the tentative primer on the single strand; or / and

[0056] drag the primer graphic or place a mouse pointer inside the primer graphic to move the horizontal position of the tentative primer on the single strand.

[0057] Preferably, the primer pattern is a frame shape enclosing the to-be-determined primer.

[0058] Preferably, a primer pattern defining the to-be-determined primer is displayed on the display screen, and the modifying and determining module is further configured to:

[0059] by moving two ends of the to-be-determined primer defined by the primer pattern to move the 5' end or / and 3' end of the to-be-determined primer;

[0060] The primer pattern is any one or a combination of any two or more of a rectangle, an irregular rectangle, and a boundary line composed of lines.

[0061] Preferably, the primer design device further comprises:

[0062] a display module configured to display a prompt interface of the to-be-determined primer on the display screen;

[0063] In particular, the display module is configured to:

[0064] when the mouse pointer hovers over the name of the to-be-determined primer or the to-be-determined primer itself, trigger the display of the prompt interface of the to-be-determined primer on the display screen; and

[0065] when the to-be-determined primer is modified, trigger the display of the prompt interface of the to-be-determined primer on the display screen, and the prompt interface is in a real-time display state.

[0066] Preferably, the modifying and determining module is further configured to:

[0067] move the horizontal position of the to-be-determined primer on the single strand and determine in real time whether the primer parameters in the prompt interface of the to-be-determined primer meet the preset conditions;

[0068] The primer design device further comprises:

[0069] a first extension module configured to, when none of the primer parameters meets the preset conditions, extend N target length base sequences respectively before and after the start and end positions of the to-be-determined primer based on the target length of the to-be-determined primer and the start and end positions of the to-be-determined primer on the single strand, N being an integer greater than or equal to 1;

[0070] a first screening module configured to screen base sequences corresponding to primer parameters meeting the preset conditions and having no overlapping sites with the double-stranded structure from the 2N target length base sequences to form a first set;

[0071] a first forming module configured to select one of the base sequences in the first set and move the to-be-determined primer to the selected base sequence to form a target primer.

[0072] Preferably, the primer design device further comprises:

[0073] a second screening module, configured to screen, from the 2N target-length base sequences, base sequences corresponding to primer parameters meeting preset conditions and having no overlapping sites with the corresponding single-strand structure to form a second set;

[0074] a second forming module, configured to, when the first set is empty, select one of the base sequences from the second set, and move the pending primer horizontally to the selected base sequence to form a target primer.

[0075] Preferably, when the N target-length base sequences are obtained by extending from the start position and to the end position respectively, if the base sequences in the corresponding direction are insufficient to obtain the N target-length base sequences, the actual number of obtained base sequences is used as the criterion.

[0076] Preferably, the modifying and determining module is further configured to:

[0077] change the number of bases in the pending primer and determine in real time whether the primer parameters in the prompt interface of the pending primer meet the preset conditions;

[0078] The primer design device further comprises:

[0079] a second extending module, configured to, when none of the primer parameters meets the preset conditions, sequentially extend P to Q bases in the direction opposite to the primer direction of the pending primer based on the target position on the single strand corresponding to the 3' end of the pending primer to form Q-P+1 base sequences, P and Q being integers greater than or equal to 1, and Q being greater than P;

[0080] a third screening module, configured to screen, from the Q-P+1 base sequences, base sequences corresponding to primer parameters meeting preset conditions and having no overlapping sites with the double-strand structure as a third set;

[0081] a primer selecting module, configured to select, from the third set, a base sequence with the shortest length as a corresponding target primer;

[0082] Preferably, P is greater than or equal to 10, and Q is less than or equal to 99.

[0083] Preferably, the primer parameters include one or more of an annealing temperature, a GC content, a number of overlapping sites, and a number of binding sites.

[0084] The application further provides an electronic device comprising:

[0085] a processor coupled with a memory, the memory storing a computer program, when the processor executes the computer program, the electronic device performs the method as described above.

[0086] The application also provides a computer readable storage medium comprising instructions which, when executed, cause the method as described above to be implemented.

[0087] Advantages of the application:

[0088] The primer design method, device and electronic equipment provided by the application can directly modify the pending primer in the base sequence, which can be selected by a primer design software or already exist in the base sequence. The prompt interface on the display screen can display the primer parameters of the pending primer in real time during the modification process. The user can directly observe the primer parameters to determine whether the pending primer is suitable. If the pending primer is suitable, the pending primer can be directly determined as the target primer to complete the primer design. Thus, the application can directly observe the process of primer design parameter change by directly operating the primer on the display screen, thereby quickly completing the primer design and improving the efficiency of primer design. The user can complete the primer design by dragging the mouse, which does not need complex operation. Therefore, users who are not familiar with the primer design software can also complete the primer design, thereby improving the user experience. BRIEF DESCRIPTION OF DRAWINGS

[0089] In order to more clearly illustrate the technical solutions in the application or the prior art, the following will briefly introduce the drawings needed to be used in the embodiments or prior art description. Obviously, the drawings in the following description are some embodiments of the application, and other drawings can be obtained by those skilled in the art without creative labor.

[0090] Fig. 1 is a flowchart of the primer design method provided by the application;

[0091] Fig. 2 is an interface diagram of the primer design software provided by the application;

[0092] Fig. 3 is a structural schematic diagram of the primer design device provided by the application.

[0093] Fig. 4 is a schematic diagram of the physical structure of the electronic equipment provided by the application. DETAILED DESCRIPTION

[0094] In order to make the purpose, technical solutions and advantages of the application more clear, the technical solutions in the application will be described clearly and completely in combination with the drawings in the application. Obviously, the described embodiments are some embodiments of the application, but not all embodiments. Based on the embodiments in the application, all other embodiments obtained by those skilled in the art without creative labor belong to the protection scope of the application.

[0095] Figure 1 is a flowchart of the primer design method provided by the present application. As shown in Figure 1, the primer design method comprises the following steps:

[0096] In step 110, a double-stranded structure of a target base sequence is obtained.

[0097] Base sequence refers to the fact that, in the structure of a DNA molecule, the number of hydrogen bonds between bases is fixed and the distance between the two strands of DNA remains unchanged, so that base pairing must follow certain rules. That is, A (adenine) must pair with T (thymine), G (guanine) must pair with C (cytosine), and vice versa. This one-to-one relationship between bases is called the base complementary pairing principle, i.e., base sequence.

[0098] Base sequence refers to the combination of bases arranged in a certain base sequence.

[0099] A DNA molecule is generally double-stranded, and when designing primers using primer design software, the double-stranded structure can be imported into the software, thereby completing data preparation and interface display of the double-stranded structure.

[0100] At this time, the imported double-stranded structure can be displayed on the display screen.

[0101] Figure 2 is an interface diagram displayed by the primer design software, which displays a double-stranded structure as shown in Figure 2.

[0102] In step 120, a tentative primer is obtained from one single strand of the double-stranded structure.

[0103] The tentative primer can be obtained from any single strand of the double-stranded structure. For example, the tentative primer can be read when the double-stranded structure is imported, or the user can newly create and obtain the primer after importing the double-stranded structure. The tentative primer is usually a primer that needs to be modified and cannot be used directly, and needs to be further modified to achieve the purpose of being usable.

[0104] In step 130, the tentative primer is modified and the primer parameters in the prompt interface of the tentative primer are determined in real time to determine whether the primer parameters meet the preset conditions.

[0105] The modification of the tentative primer can include moving the horizontal position of the tentative primer on the single strand and / or changing the number of bases in the tentative primer.

[0106] We do not limit other modification methods, but we can achieve the following: for any modification, the prompt interface can display the primer parameters of the tentative primer in real time during the modification process.

[0107] The primer parameters include one or more of annealing temperature, GC content, number of overlapping sites, and number of binding sites.

[0108] The above primer parameters are only some of the optimal parameters involved in the embodiment, and other parameters can also be used, which are all within the protection scope of the present application.

[0109] The preset conditions correspond to the primer parameters, such as whether the annealing temperature is about 60 degrees, at least between 55-80 degrees; the GC content is generally 40%-60%, preferably 45%-55%; and the number of overlapping sites and the number of binding sites are as close to zero as possible.

[0110] The corresponding primer parameters can have corresponding preset conditions, such as the length of the primer is generally 15-30 bp, and other parameters can also be included, which are not described in detail.

[0111] In step 140, when the primer parameters meet the preset conditions, the corresponding tentative primer is determined as the target primer.

[0112] Based on the above preset conditions, when the preset conditions are met, it indicates that the tentative primer meets the requirements and can be determined as the target primer.

[0113] It can be understood that when the tentative primer obtained from step 120 meets the preset conditions without any modification at the beginning, the tentative primer is the target primer, and at this time, it can be understood that the modification content is empty.

[0114] According to the above method, for the tentative primer in the base sequence, the tentative primer can be a segment selected by a primer design software or a segment already existing in the base sequence. When designing the tentative primer, the tentative primer can be directly modified. During the modification process, the prompt interface on the display screen can display the primer parameters of the tentative primer in real time, and the user can directly observe the primer parameters to determine whether the tentative primer is suitable. If it is suitable, the tentative primer can be directly determined as the target primer to complete the primer design. Therefore, the present application can directly observe the process of primer design parameter change by directly operating the primer on the display screen, thereby quickly completing the primer design and improving the efficiency of primer design. The user can complete the primer design by dragging the mouse, without complex operation, so that users who are not familiar with the primer design software can also complete the primer design, thereby improving the user experience.

[0115] In one embodiment, step 120 obtains the tentative primer from one single strand of the double-stranded structure, including:

[0116] Selecting a continuous base sequence as the candidate primer from one single strand of the double-stranded structure by box selection, single selection, or a combination of box selection and single selection.

[0117] The user can have the candidate primer data directly when establishing the double-stranded data, so that the candidate primer data is directly displayed on the display screen, at this time, the obtained candidate primer can be directly displayed on the display screen, that is, the displayed candidate primer is the obtained candidate primer.

[0118] The user can also select from the double-stranded structure displayed on the display screen, that is, select by box selection, single selection, or a combination of box selection and single selection as described above.

[0119] Box selection refers to continuous one-time selection of multiple bases, and single selection refers to one-by-one selection of bases, and the two methods can be used arbitrarily.

[0120] As shown in FIG. 2, a plurality of primers such as primer name K32.FOR are displayed, and these primers can be obtained by the above method. The above method can obtain the candidate primer more quickly.

[0121] Generally, the name of the candidate primer is displayed on the display screen, and the horizontal position of the candidate primer on the single strand is moved by:

[0122] Dragging the name of the candidate primer to move the horizontal position of the candidate primer on the single strand.

[0123] As shown in FIG. 2, K32.FOR and K33.FOR are primer names, and the mouse cursor can be placed on the primer name to move the horizontal position of the candidate primer on the single strand. This method can quickly move the primer in the horizontal position, thereby adjusting the horizontal position of the primer.

[0124] In one embodiment, the display screen displays a primer graphic that defines the candidate primer, as shown in FIG. 2, the primers K32.FOR and K33.FOR are wrapped by the primer graphic, and the horizontal position of the candidate primer on the single strand is moved by:

[0125] Dragging the primer graphic or placing the mouse pointer inside the primer graphic to move the horizontal position of the candidate primer on the single strand.

[0126] The primer graphic is a frame shape that frames the candidate primer.

[0127] The horizontal movement of the primer can be achieved by the above different methods, which facilitates the user to achieve horizontal movement by different methods, facilitates the user operation, and improves the operation experience.

[0128] In one embodiment, the changing the number of bases in the pending primer includes:

[0129] moving the 5' end or / and 3' end of the pending primer to increase or decrease the number of bases in the pending primer.

[0130] The number of bases in the pending primer can be increased or decreased, and specifically, the increase or decrease of bases can be controlled at the 5' end of the pending primer or at the 3' end of the pending primer. This way of controlling the change in the number of bases facilitates the user to control the number of bases and quickly modify the primer.

[0131] In one embodiment, the display screen displays a primer graphic defining the pending primer, and the moving the 5' end or / and 3' end of the pending primer specifically includes:

[0132] The moving the 5' end or / and 3' end of the pending primer is achieved by moving the two ends of the pending primer defined by the primer graphic.

[0133] When the user moves the 5' end or / and 3' end, the moving the 5' end or / and 3' end of the pending primer can be achieved by moving the two ends of the pending primer defined by the primer graphic, as shown in FIG. 2, the position of the mouse cursor is displayed in the upper left corner, which is at the 3' end defined by the primer graphic, and the prompt interface prompts "Drag to move primer", at this time, the 3' end defined by the primer graphic can be moved to achieve the increase or decrease of bases.

[0134] This way can more quickly achieve the operation of the bases, thereby quickly increasing or decreasing the number of bases and improving the convenience of primer design.

[0135] In one embodiment, the primer graphic is any one or any two or more combinations of a rectangular shape, an irregular rectangular shape, and a boundary line composed of lines.

[0136] As shown in FIG. 2, the primer graphic is a rectangular shape, but the present embodiment is not limited to the above shape. The primer graphic can better achieve the operation of the primer, and the present embodiment preferably adopts the graphic shown in FIG. 2.

[0137] In one embodiment, the primer design method further includes:

[0138] The prompt interface of the pending primer is displayed on the display screen.

[0139] The triggering of the prompt interface includes various situations, and the prompt interface includes primer parameters, so that the user can directly view the information of the primer through the prompt interface, thereby facilitating the modification of the primer.

[0140] In one embodiment, when the mouse pointer hovers over the name of the pending primer or the pending primer itself, a prompt interface of the pending primer is displayed on the display screen. This is a static prompt interface, which facilitates the user to view the related parameters of the primer in real time.

[0141] When the pending primer is modified, a prompt interface of the pending primer is displayed on the display screen, and the prompt interface is in a real-time display state. This is a dynamic prompt interface, which facilitates the user to view the parameters in real time during the operation of the primer, thereby quickly realizing the design of the primer.

[0142] In one embodiment, when the pending primer is modified and the primer parameters in the prompt interface of the pending primer are determined in real time whether they meet the preset conditions, the method comprises:

[0143] The horizontal position of the pending primer on the single strand is moved, and the primer parameters in the prompt interface of the pending primer are determined in real time whether they meet the preset conditions.

[0144] The primer design method further comprises:

[0145] When none of the primer parameters meets the preset conditions, based on the target length of the pending primer and the start and end positions of the pending primer on the single strand, N target length base sequences are obtained by extending forward and backward from the start and end positions respectively, and N is an integer greater than or equal to 1.

[0146] From the 2N target length base sequences, base sequences corresponding to primer parameters meeting the preset conditions and having no overlapping sites with the double-stranded structure are selected to form a first set.

[0147] One of the base sequences in the first set is selected, and the pending primer is moved horizontally to the selected base sequence to form a target primer.

[0148] The user can not be able to accurately obtain the required target primer by moving the mouse horizontally, especially when the base sequence is long. At this time, the target primer can be quickly determined by the above method. That is, N target length base sequences are obtained by extending forward and backward from the start and end positions of the 5' end and 3' end of the pending primer on the base sequence, and a first set is selected from them. This way can quickly confirm the target primer, especially when the base sequence is long.

[0149] In one embodiment, after the 2N target length base sequences are obtained by extending forward and backward from the start and end positions respectively, the primer design method further comprises:

[0150] From the 2N target length base sequences, base sequences corresponding to primer parameters meeting the preset conditions and having no overlapping sites with the corresponding single-stranded structure are selected to form a second set.

[0151] When the first set is empty, then one of the base sequences in the second set is selected, and the pending primer is horizontally moved to the selected base sequence to form a target primer.

[0152] When the first set is empty, it means that there is no suitable primer, at this time, the second set can be formed by the above method to determine the primer. This way can get better primers when the first set is empty, giving users a better choice.

[0153] In one embodiment, when the start and end positions are respectively extended to obtain N target length base sequences, if the corresponding direction base sequence is not enough to obtain N target length base sequences, the actual number obtained is used.

[0154] As shown in FIG. 2, the left side of primer K32.FOR has fewer bases. When N is large, it is not possible to obtain bases from the left side. At this time, the actual number of bases obtained is used. This way can ensure that the obtained bases are in the sequence, and ensure that the final primer can take effect.

[0155] In one embodiment, the pending primer is modified and the primer parameters in the prompt interface of the pending primer are determined in real time to determine whether they meet the preset conditions, including:

[0156] The number of bases in the pending primer is changed, and the primer parameters in the prompt interface of the pending primer are determined in real time to determine whether they meet the preset conditions.

[0157] The primer design method further includes:

[0158] When none of the primer parameters meet the preset conditions, then based on the target position on the single strand corresponding to the 3' end of the pending primer, the target position is sequentially extended from P to Q bases in the opposite direction of the primer direction of the pending primer to form Q-P+1 base sequences. P and Q are integers greater than or equal to 1, and Q is greater than P;

[0159] From the Q-P+1 base sequences, the base sequence corresponding to the primer parameter meeting the preset condition and having no overlapping site with the pending primer corresponding single strand is selected as a third set;

[0160] The base sequence with the shortest sequence in the third set is selected as the corresponding target primer;

[0161] Preferably, P is greater than or equal to 10, and Q is less than or equal to 99.

[0162] When the user cannot obtain the target primer by changing the number of bases, the target primer can be obtained by searching, as shown in FIG. 2. By the above method, the primer K32.FOR can be extended by P bases to the right of the 3' end, P is preferably 10, and Q is preferably 99, then a sequence of Q-P+1 bases is formed, and a suitable primer is selected from the sequence, and the shortest primer can be selected. This way not only can quickly obtain the primer, but also is convenient for the user to operate.

[0163] The embodiment also provides a primer design device, comprising:

[0164] a structure obtaining module 110, configured to obtain a double-stranded structure of a target base sequence;

[0165] a primer obtaining module 120, configured to obtain a to-be-determined primer from one single strand of the double-stranded structure;

[0166] a modifying and determining module 130, configured to modify the to-be-determined primer and determine whether a primer parameter in a prompt interface of the to-be-determined primer meets a preset condition in real time;

[0167] a target module 140, configured to take the corresponding to-be-determined primer as a determined target primer when the primer parameter meets the preset condition.

[0168] The primer design device can be used to select a to-be-determined primer from a base sequence, modify the to-be-determined primer, and determine whether the to-be-determined primer is suitable by observing a primer parameter of the to-be-determined primer in a prompt interface of a display screen in real time, and if the to-be-determined primer is suitable, the to-be-determined primer can be directly determined as a target primer to complete primer design. Thus, the primer design parameter change process can be directly observed by directly operating the primer on the display screen, and the primer design can be quickly completed, thereby improving the efficiency of primer design. The user can complete the primer design by dragging a mouse, without complex operation, so that a user who is not familiar with primer design software can also complete the primer design, thereby improving the user experience.

[0169] In one embodiment, the primer obtaining module 120 is specifically configured to select a continuous base sequence as a to-be-determined primer from one single strand of the double-stranded structure by framing, single selection, or a common way of framing and single selection.

[0170] In one embodiment, the modifying and determining module 130 is specifically configured to:

[0171] move a horizontal position of the to-be-determined primer on the single strand; and / or

[0172] changing the number of bases in the pending primer.

[0173] In one embodiment, the display screen displays the name of the pending primer, and the modifying and determining module 130 is further configured to:

[0174] dragging the name of the pending primer to move the horizontal position of the pending primer on the single strand.

[0175] In one embodiment, the display screen displays a primer figure defining the pending primer, and the modifying and determining module 130 is further configured to:

[0176] dragging the primer figure or placing the mouse pointer inside the primer figure to move the horizontal position of the pending primer on the single strand.

[0177] In one embodiment, the modifying and determining module 130 is further configured to:

[0178] moving the 5' end or / and 3' end of the pending primer to increase or decrease the number of bases in the pending primer.

[0179] In one embodiment, the display screen displays a primer figure defining the pending primer, and the modifying and determining module 130 is further configured to:

[0180] moving the 5' end or / and 3' end of the pending primer by moving the two ends of the pending primer defined by the primer figure.

[0181] In one embodiment, the primer figure is any one or any two or more combinations of a rectangle, an irregular rectangle, and a boundary line composed of lines.

[0182] In one embodiment, the primer design device further comprises:

[0183] a display module configured to display a prompt interface of the pending primer on the display screen.

[0184] In one embodiment, the display module is configured to:

[0185] when the mouse pointer hovers over the name of the pending primer or the pending primer itself, triggering the display of the prompt interface of the pending primer on the display screen; and

[0186] when the pending primer is modified, triggering the display of the prompt interface of the pending primer on the display screen, and the prompt interface is in a real-time display state.

[0187] In one embodiment, the modifying and determining module is further configured to:

[0188] moving a horizontal position of the pending primer on the single strand and determining in real time whether the primer parameters in the prompt interface of the pending primer meet preset conditions;

[0189] The primer design apparatus further comprises:

[0190] The first extension module is configured to, when none of the primer parameters meets the preset conditions, respectively extend from and to the start and end positions to obtain N target length base sequences based on the target length of the pending primer and the start and end positions on the single strand, N being an integer greater than or equal to 1.

[0191] The first screening module is configured to screen base sequences corresponding to primer parameters meeting the preset conditions and having no overlapping sites with the double-stranded structure from the 2N target length base sequences to form a first set.

[0192] The first forming module is configured to select one of the base sequences in the first set and move the pending primer horizontally to the selected base sequence to form a target primer.

[0193] In one embodiment, the primer design apparatus further comprises:

[0194] The second screening module is configured to screen base sequences corresponding to primer parameters meeting the preset conditions and having no overlapping sites with the corresponding single-stranded structure from the 2N target length base sequences to form a second set.

[0195] The second forming module is configured to, when the first set is empty, select one of the base sequences in the second set and move the pending primer horizontally to the selected base sequence to form a target primer.

[0196] In one embodiment, when the N target length base sequences are respectively obtained by extending from and to the start and end positions, if the base sequences in the corresponding direction are insufficient to obtain the N target length base sequences, the actual number of base sequences obtained is used.

[0197] In one embodiment, the modifying and determining module is further configured to:

[0198] change the number of bases in the pending primer and determine in real time whether the primer parameters in the prompt interface of the pending primer meet preset conditions;

[0199] The primer design apparatus further comprises:

[0200] a second extending module, configured to, when none of the primer parameters meets the preset condition, extend P to Q bases in the reverse direction of the primer direction of the pending primer based on the target position on the single strand corresponding to the 3' end of the pending primer, to form Q-P+1 base sequences, P and Q being integers greater than or equal to 1, and Q being greater than P;

[0201] a third screening module, configured to screen, from the Q-P+1 base sequences, base sequences corresponding to primer parameters meeting the preset condition and having no overlapping sites with the double-stranded structure as a third set;

[0202] a primer selecting module, configured to select, from the third set, a base sequence with the shortest length as a target primer corresponding thereto;

[0203] Preferably, P is greater than or equal to 10, and Q is less than or equal to 99.

[0204] In one embodiment, the primer parameters include one or more of an annealing temperature, a GC content, a number of overlapping sites, and a number of binding sites.

[0205] The specific details of the modules / units in the above apparatus have been described in the method embodiments, and the undisclosed details can be referred to the method embodiments, and thus will not be described here.

[0206] Those skilled in the art can understand that each aspect of the present disclosure can be implemented as a system, a method or a program product. Therefore, each aspect of the present disclosure can be embodied as a whole hardware embodiment, a whole software embodiment (including firmware, microcode, etc.), or an embodiment combining software and hardware aspects, which can be collectively referred to as "circuitry", "module" or "system".

[0207] The present embodiment also provides an electronic device, comprising:

[0208] a processor coupled with a memory, the memory storing a computer program, when the processor executes the computer program, causing the electronic device to perform the method as described above.

[0209] The present embodiment also provides a computer readable storage medium, characterized in that the computer readable storage medium includes instructions, when the instructions are executed, causing the method as described above to be implemented.

[0210] Fig. 4 shows a schematic diagram of an electronic device, which can include a processor 310, a communications interface 320, a memory 330 and a communications bus 340, wherein the processor 310, the communications interface 320 and the memory 330 can communicate with each other through the communications bus 340. The processor 310 can invoke the logical instructions in the memory 330 to execute the above-mentioned primer design method, which includes: obtaining a double-stranded structure of a target base sequence; obtaining a tentative primer from one single strand of the double-stranded structure; modifying the tentative primer and determining whether a primer parameter in a prompt interface of the tentative primer meets a preset condition in real time; and when the primer parameter meets the preset condition, taking the corresponding tentative primer as a determined target primer.

[0211] In addition, the logical instructions in the memory 330 described above can be implemented in the form of a software functional unit and sold or used as an independent product, which can be stored in a computer-readable storage medium. Based on this understanding, the technical solutions of the present application essentially or the part that contributes to the prior art or part of the technical solutions can be embodied in the form of a software product, which is stored in a storage medium, includes several instructions to make a computer device (which can be a personal computer, a server, or a network device, etc.) execute all or part of the steps of the methods described in various embodiments of the present application. The aforementioned storage medium includes: a U disk, a mobile hard disk, a read-only memory (ROM, Read-Only Memory), a random access memory (RAM, Random Access Memory), a magnetic disk or an optical disk, and various media that can store program codes.

[0212] On the other hand, the present application also provides a computer program product, which includes a computer program, the computer program can be stored on a non-transitory computer readable storage medium, and the computer program can be executed by a processor to make a computer execute the primer design method provided by the above-mentioned methods, which includes: obtaining a double-stranded structure of a target base sequence; obtaining a tentative primer from one single strand of the double-stranded structure; modifying the tentative primer and determining whether a primer parameter in a prompt interface of the tentative primer meets a preset condition in real time; and when the primer parameter meets the preset condition, taking the corresponding tentative primer as a determined target primer.

[0213] In another aspect, the present invention also provides a non-transitory computer-readable storage medium storing a computer program thereon, which, when executed by a processor, implements the primer design method provided by the above methods. The method includes: obtaining a double-stranded structure of a target base sequence; obtaining a primer to be determined from a single strand of the double-stranded structure; modifying the primer to be determined and determining in real time whether the primer parameters in the prompt interface of the primer to be determined meet preset conditions; when the primer parameters meet the preset conditions, using the corresponding primer to be determined as the target primer.

[0214] The device embodiments described above are merely illustrative. The units described as separate components may or may not be physically separate. The components shown as units may or may not be physical units; that is, they may be located in one place or distributed across multiple network units. Some or all of the modules can be selected to achieve the purpose of this embodiment according to actual needs. Those skilled in the art can understand and implement this without any creative effort.

[0215] Through the above description of the embodiments, those skilled in the art can clearly understand that each embodiment can be implemented by means of software plus necessary general-purpose hardware platforms, and of course, it can also be implemented by hardware. Based on this understanding, the above technical solutions, in essence or the part that contributes to the prior art, can be embodied in the form of a software product. This computer software product can be stored in a computer-readable storage medium, such as ROM / RAM, magnetic disk, optical disk, etc., and includes several instructions to cause a computer device (which may be a personal computer, server, or network device, etc.) to execute the methods described in the various embodiments or some parts of the embodiments.

[0216] Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention, and not to limit them; although the present invention has been described in detail with reference to the foregoing embodiments, those skilled in the art should understand that modifications can still be made to the technical solutions described in the foregoing embodiments, or equivalent substitutions can be made to some of the technical features; and these modifications or substitutions do not cause the essence of the corresponding technical solutions to deviate from the spirit and scope of the technical solutions of the embodiments of the present invention.

Claims

1. A primer design method, characterized by, The method comprises: obtaining a double-stranded structure of a target base sequence; obtaining a tentative primer from one single strand of the double-stranded structure; modifying the tentative primer and determining in real time whether a primer parameter in a prompt interface of the tentative primer meets a preset condition; when the primer parameter meets the preset condition, taking the corresponding tentative primer as a determined target primer.

2. The primer design method of claim 1, wherein, The step of obtaining a tentative primer from one single strand of the double-stranded structure comprises: selecting a continuous base sequence as a tentative primer from one single strand of the double-stranded structure by means of box selection, single selection, or a combination of box selection and single selection.

3. The primer design method of claim 1, wherein, The step of modifying the tentative primer comprises: moving a horizontal position of the tentative primer on the single strand; and / or changing a base number in the tentative primer, preferably by moving a 5' end or / and a 3' end of the tentative primer to increase or decrease the base number in the tentative primer.

4. The primer design method of claim 3, wherein, The display screen displays a name of the tentative primer and / or a primer figure defining the tentative primer, and the step of moving the horizontal position of the tentative primer on the single strand comprises: dragging the name of the tentative primer to move the horizontal position of the tentative primer on the single strand; and / or dragging the primer figure or placing a mouse pointer inside the primer figure to move the horizontal position of the tentative primer on the single strand; preferably, the primer figure is a box shape that boxes the tentative primer.

5. The primer design method according to claim 3, wherein, The display screen displays a primer figure defining the tentative primer, and the step of moving the 5' end or / and the 3' end of the tentative primer comprises: moving two ends of the tentative primer defined by the primer figure to move the 5' end or / and the 3' end of the tentative primer; preferably, the primer figure is any one or a combination of more than two of a rectangular shape, an irregular rectangular shape, and a boundary line composed of lines.

6. The primer design method according to any one of claims 1 to 5, wherein, The primer design method further comprises: displaying a prompt interface of the tentative primer on the display screen; the step of displaying the prompt interface of the tentative primer on the display screen comprises: triggering the display of the prompt interface of the tentative primer on the display screen when a mouse pointer hovers over the name of the tentative primer or the tentative primer itself; and when the tentative primer is modified, the prompt interface of the tentative primer is triggered to be displayed on the display screen, and the prompt interface is in a real-time display state.

7. The primer design method of claim 1, wherein, The step of modifying the tentative primer and determining in real time whether a primer parameter in a prompt interface of the tentative primer meets a preset condition comprises: moving the horizontal position of the tentative primer on the single strand and determining in real time whether a primer parameter in a prompt interface of the tentative primer meets a preset condition; The primer design method further comprises: when none of the primer parameters meets the preset condition, then based on a target length of the tentative primer and start and end positions of the tentative primer on the single strand, extending respectively forward and backward from the start and end positions to obtain N base sequences of the target length, N being an integer greater than or equal to 1; screening base sequences from 2N base sequences of the target length to form a first set, the base sequences meeting the preset condition of the primer parameter and having no overlapping sites with the double-stranded structure; and selecting a target primer from the first set. select one of the base sequences from the first set and move the pending primer horizontally to the selected base sequence to form a target primer. Further, after the base sequences of N target lengths are obtained by extending from the start position and the end position respectively, the primer design method further comprises: selecting base sequences corresponding to the primer parameters meeting the preset conditions and having no overlapping sites with the corresponding single-stranded structure from the 2N base sequences of target lengths to form a second set; when the first set is empty, selecting one of the base sequences from the second set and moving the pending primer horizontally to the selected base sequence to form a target primer.

8. The primer design method of claim 7, wherein, When the base sequences of N target lengths are obtained by extending from the start position and the end position respectively, if the base sequences in the corresponding direction are insufficient to obtain the base sequences of N target lengths, the actual number obtained is used as the criterion.

9. The primer design method of claim 1, wherein, The modification and determination module is configured to modify the pending primer and determine in real time whether the primer parameters in the prompt interface of the pending primer meet the preset conditions. The modification and determination module is configured to modify the pending primer and determine in real time whether the primer parameters in the prompt interface of the pending primer meet the preset conditions. The primer design method further comprises: When none of the primer parameters meets the preset conditions, extending P to Q bases in the reverse direction of the primer direction of the pending primer from the target position on the corresponding single strand of the 3' end of the pending primer in sequence to form Q-P+1 base sequences, P and Q are integers greater than or equal to 1, and Q is greater than P; selecting base sequences corresponding to the primer parameters meeting the preset conditions and having no overlapping sites with the corresponding single-stranded structure from the 2N base sequences of target lengths to form a second set; selecting the base sequence with the shortest length from the third set as the corresponding target primer; Preferably, P is greater than or equal to 10, and Q is less than or equal to 99.

10. The primer design method according to any one of claims 1 to 9, wherein, The primer parameters include one or more of annealing temperature, GC content, number of overlapping sites, and number of binding sites.

11. A primer design apparatus characterized by comprising: The primer design method further comprises: a structure obtaining module configured to obtain the double-stranded structure of the target base sequence; a primer obtaining module configured to obtain a pending primer from one single strand of the double-stranded structure; a modification and determination module configured to modify the pending primer and determine in real time whether the primer parameters in the prompt interface of the pending primer meet the preset conditions; a target module configured to use the corresponding pending primer as a determined target primer when the primer parameters meet the preset conditions.

12. The primer design apparatus of claim 11, wherein, The primer obtaining module is specifically configured to select a continuous base sequence as a pending primer from one single strand of the double-stranded structure by framing, single selection, or a common method of framing and single selection.

13. The primer design method of claim 11, wherein, The modification and determination module is specifically configured to: move the horizontal position of the pending primer on the single strand; and / or change the number of bases in the pending primer; The change in the number of bases in the pending primer includes moving the 5' end or / and 3' end of the pending primer to increase or decrease the number of bases in the pending primer.

14. The primer design apparatus of claim 13, wherein, The modification and determination module is further configured to: display the name of the pending primer or / and a primer graph defining the pending primer on the display screen. dragging the name of the pending primer to move the horizontal position of the pending primer on the single strand; or / and dragging the primer figure or placing the mouse pointer inside the primer figure to move the horizontal position of the pending primer on the single strand; Preferably, the primer figure is a frame shape enclosing the pending primer.

15. The primer design apparatus of claim 13, wherein, The display screen displays a primer figure defining the pending primer, and the modifying and determining module is further configured to: move the 5' end or / and 3' end of the pending primer by moving the two ends of the pending primer defined by the primer figure; Preferably, the primer figure is any one or a combination of any two or more of a rectangle shape, an irregular rectangle shape and a boundary line composed of lines.

16. The primer design device of any one of claims 11-15, wherein, The primer design device further comprises: a display module configured to display a prompt interface of the pending primer on a display screen; Preferably, the display module is configured to: trigger the display of the prompt interface of the pending primer on the display screen when the mouse pointer hovers over the name of the pending primer or the pending primer itself; and trigger the display of the prompt interface of the pending primer on the display screen when the pending primer is being modified, and the prompt interface is in a real-time display state.

17. The primer design apparatus of claim 11, wherein, The modifying and determining module is further configured to: move the horizontal position of the pending primer on the single strand and determine in real time whether the primer parameters in the prompt interface of the pending primer meet the preset conditions; The primer design device further comprises: a first extension module configured to, when none of the primer parameters meets the preset conditions, extend respectively before and after the start and end positions to obtain N target length base sequences based on the target length of the pending primer and the start and end positions on the single strand corresponding to the pending primer, N being an integer greater than or equal to 1; a first screening module configured to screen base sequences corresponding to primer parameters meeting the preset conditions and having no overlapping sites with the double-stranded structure from 2N target length base sequences to form a first set; a first forming module configured to select one of the base sequences from the first set and move the pending primer horizontally to the selected base sequence to form a target primer; Further, the primer design device further comprises: a second screening module configured to screen base sequences corresponding to primer parameters meeting the preset conditions and having no overlapping sites with the corresponding single-stranded structure from 2N target length base sequences to form a second set; a second forming module configured to, when the first set is empty, select one of the base sequences from the second set and move the pending primer horizontally to the selected base sequence to form a target primer.

18. The primer design apparatus of claim 17, wherein, When extending respectively before and after the start and end positions to obtain N target length base sequences, if the base sequences in the corresponding direction are insufficient to obtain N target length base sequences, the actual number obtained is used.

19. The primer design apparatus of claim 11, wherein, The modifying and determining module is further configured to: change the number of bases in the pending primer and determine in real time whether the primer parameters in the prompt interface of the pending primer meet the preset conditions; The primer design device further comprises: a second extending module, configured to, when none of the primer parameters meets the preset condition, sequentially extend P to Q bases from a target position on a single strand corresponding to the 3' end of the pending primer in a direction opposite to a primer direction of the pending primer to form Q-P+1 base sequences, P and Q being integers greater than or equal to 1, and Q being greater than P; a third screening module, configured to screen, from the Q-P+1 base sequences, a base sequence corresponding to a primer parameter meeting the preset condition and having no overlapping site with the double-stranded structure as a third set; a primer selecting module, configured to select, from the third set, a base sequence with the shortest length as a corresponding target primer; Preferably, P is greater than or equal to 10, and Q is less than or equal to 99.

20. The primer design device of any one of claims 11-20, wherein, The primer parameters include one or more of an annealing temperature, a GC content, a number of overlapping sites, and a number of binding sites.

21. An electronic device, comprising: comprising a processor coupled to a memory, the memory storing a computer program, when the processor executes the computer program, the electronic device executes the method in any one of claims 1 to 10.

22. A computer-readable storage medium, characterized in that, The computer readable storage medium includes instructions, when the instructions are executed, the method in any one of claims 1 to 10 is implemented.

Images