Method for determining optimal sequence alignment threshold for gene database

Abstract

The invention discloses a method for determining an optimal sequence alignment threshold for a gene database. The method comprises the following steps: 1) acquiring a protein sequence; 2) removing sequences included in the gene database from the protein sequences, and creating a pseudogene data set; 3) dividing protein sequences in the gene database into subclasses to serve as a true gene data set; 4) combining the pseudogene data set and the true gene data set, and simulating a DNA sequence with a specific length generated by high-throughput sequencing for any protein sequence to obtain a simulated data set; 5) performing sequence comparison, and comparing a comparison threshold value to obtain a value; 6) judging a sequence comparison result, and calculating the numbers of true positive,mismatch, false positive, false negative and true negative; 7) calculating sensitivity, accuracy and a Mathesian correlation coefficient; 8) drawing a three-dimensional curved surface graph by takingthe similarity as an X axis, the E value as a Y axis and the sensitivity, the accuracy or the Malaysian correlation coefficient as a Z axis; and 9) determining an optimal sequence alignment thresholdof the gene database in the three-dimensional curved surface graph.

Description

technical field [0001] The invention belongs to the field of biotechnology, and relates to a method for determining the optimal sequence comparison threshold for a gene database by combining means such as simulation data set construction and sequence comparison effect evaluation. Background technique [0002] In recent years, high-throughput sequencing technology has developed rapidly. Because of its advantages of high throughput, high accuracy, and rich information, high-throughput sequencing technology is widely used in microbial ecology research to explore the diversity, community structure, and ecological functions of complex microbial communities. In particular, high-throughput sequencing technology solves the problem that most microorganisms cannot be isolated and cultured, and provides a powerful technical means for the research on the metabolic potential and ecological function of these microorganisms. [0003] The use of high-throughput sequencing technology to obt...

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Problems solved by technology

[0006] Aiming at the current problem of selecting the optimal sequence alignment threshold (similarity and E value) for gene databases generally based on empiricism, the present invention proposes for the first time that all protein sequences of protein sequence databases (for example, Swiss-Prot protein sequence database) are used Construct a simulated data set, compare the simulated sequences in the gene database, and evaluate the sequence alignment effect with sensitivity, accuracy and Matthews correlation coefficient (MCC), so as to provide a rapid and scientific basis for the gene database Key Techniques for Determining Optimal Sequence Alignment Thresholds (i.e., Similarity and E Value)

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