Method for identifying SNP in individual in Sanger sequencing oriented to PCR products of diploid

Abstract

The invention discloses a method for identifying SNP in an individual in Sanger sequencing oriented to PCR products of diploid. According to the method, firstly, fluorescent data of four bases of adenine A, guanine G, cytosine C and thymine T contained in a chromatogram map are independently separated, filtering and noise reduction processing is carried out on the separated fluorescent data by adopting a small wave multiscale analysis method; the waveform characteristics of the fluorescent data of the four bases are further analyzed, a first peak and a second peak of the waveform are detected, and the peak distance, the height specific value and the fluctuation degree specific value of the waveform characteristics are selected as the elements for judging SNP loca, a BP nerve net with the structure of 3-10-1 is selected as a classifier for the detection of the SNP loca, and training is carried out on the BP nerve net by adopting a Levenberg Marquardt algorithm; output is mapped as SNP evaluation scores from 0 to 100 by adopting piecewise linear transformation, the classification of the SNP loca is defined from a 1 level to a 5 level according to the evaluation scores, and the SNP confidence coefficient of the loca is judged according to the classification. The method for identifying the SNP in the individual in the Sanger sequencing oriented to the PCR products of the diploid can effectively detect the SNP loca in the individuals in sequencing files.

Description

technical field [0001] The invention belongs to the field of computer automatic recognition, relates to bioinformatics, pattern recognition, statistics, signal processing and computer software technology, and in particular relates to a method for targeting diploid polymerase chains when there is no reference sequence and only a few samples. A method for identifying single nucleotide polymorphisms (Single nucleotide polymorphisms, SNPs) within individuals in Sanger sequencing of Polymerase chain reaction (PCR) products. Background technique [0002] SNP refers to the variation (or polymorphism) caused by the substitution of a single nucleotide at the level of genetic material DNA. SNP has the characteristics of universality, representativeness, heredity, stability, etc., and reflects rich genetic information. The most common heritable variation, SNPs have also become widely used genetic markers. SNPs may lead to differences in individual phenotypes. For example, SNPs may be ...

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Problems solved by technology

However, none of these software can analyze a single sequencing file. For example, novoSNP and Mutation Surveyor require a reference sequence, which is not feasible when the reference gene sequence is sequenced and the measured sequence has introns (not in the gene sequence); PolyPhred5. 0 The comparison of more than 8 sequencing files is required to accurately interpret the SNP, which is not suitable for sequencing of a single or a small number of samples

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