A method and device for automatic sequence splicing
An automatic splicing and sequencing technology, applied in sequence analysis, bioinformatics, instruments, etc., can solve the problems of splicing result error and splicing result interference, and achieve the effect of improving accuracy and eliminating random repeating sequences.
Active Publication Date: 2019-07-26
GENEWIZ INC SZ
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In addition, the mismatch of repeated sequences may interfere with the splicing results; in addition, the error signal of the sequencing data itself and the selection of the splicing starting piece will cause errors in the splicing results
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[0032] Below, in conjunction with accompanying drawing and specific embodiment, the present invention is described further:
[0033] like figure 1 As shown, the present invention provides an automatic sequence splicing method, which is applied to an automatic sequence splicing system, and the system includes three parts, namely an input module, a sequence splicing main program and an output module.
[0034] The input module is used to provide the customer with an input interface for obtaining the sequencing samples input by the user; the main program of sequence splicing is used to splice the sequences and generate a sequencing result file; the output module is used to Display the stitching result to the user. The splicing result includes instructions for using the splicing result of each sequencing sample and suggestions on whether it is available, and supports downloading of splicing results in multiple formats. The splicing results are detailed in Table 1 below:
[0035]...
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The invention discloses a sequence automatic splicing method and apparatus. The method comprises the following steps of S1, obtaining a sequencing sample and preprocessing the sequencing sample, wherein the sequencing sample comprises a plurality of sequencing data sequences; S2, calculating the length of each sequencing data sequence, and selecting the sequencing data sequence with the maximum length as an initial sequence; S3, selecting one sequencing data sequence from the rest of the sequencing data sequences and marking the sequencing data sequence as a to-be-spliced sequence; S4, comparing the initial sequence with the to-be-spliced sequence; S5, when the initial sequence and the to-be-spliced sequence have a common substring with the length greater than a preset value M, splicing the initial sequence and the to-be-spliced sequence to obtain a spliced sequence, and marking the spliced sequence as a new initial sequence; S6, judging whether the non-spliced sequencing data sequences exist or not, and if yes, executing the steps S3, S4 and S5; if not, executing the step S7; and S7, generating a sequencing result file. According to the method and the apparatus, the accuracy of a splicing result is greatly improved.
Description
technical field [0001] The present invention relates to biological DNA sequences, in particular to a method and device for splicing sequences. Background technique [0002] Generally speaking, the sequence assembly process can usually be divided into the following stages: 1. Overlapping stage, in which each fragment is compared with other fragments to find the overlapping part; 2. Layout stage, combining all fragments Form an approximate multiple alignment; 3. Consensus stage, determine the final complete sequence. When the number of sequence fragments is large, calculating the overlap of all sequence combinations will bring a computational bottleneck, so more efficient calculation methods are needed. In addition, the mismatch of repeated sequences is likely to interfere with the splicing results; in addition, the error signal of the sequencing data itself and the selection of the splicing starting piece will cause errors in the splicing results. Contents of the invention...
Claims
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IPC IPC(8): G16B30/00
CPCG16B30/00
Inventor 段广有金亮徐凤丹廖国娟葛毅
Owner GENEWIZ INC SZ