Method and system for intelligent enzyme digestion simulation based on BM matching algorithm and PSO optimization algorithm

Abstract

The invention discloses a method for intelligent enzyme digestion simulation based on a BM matching algorithm and a PSO optimization algorithm. The method comprises the steps that (1) the BM algorithm is used for simulating single enzyme or multienzyme digestion in a large scale efficiently, the cohesive end information and the base sequence of each enzyme digestion section are obtained, and the problem of limitation of genome size of an existing enzyme digestion tool is solved; (2) enzyme digestion section size, GC content and base balance are subjected to counting and displaying, so that the amplification efficiency of sections with certain length is evaluated; (3) an electrophoretogram mode is used for showing enzyme digestion simulation results, and enzyme digestion simulation effects are shown vividly; (4) the ratio of certain sequences in a certain length range is subjected to computing and counting, and a foundation and supporting are provided for certain base or sequence target sequencing; and (5) an optimal solution algorithm PSO is used for optimizing selecting of the area range of enzyme digestion, and accordingly target base or feature sequence sequencing efficiency from a selected area range is highest. Finally, the results are collected to form an assessment report in a webpage mode, and a researcher and a user can know the enzyme digestion simulation effect clearly and conveniently.

Description

technical field [0001] The invention belongs to the technical field of genetic engineering, and in particular relates to a method and system for intelligently simulating enzyme digestion based on a BM matching algorithm and a PSO optimization algorithm. Background technique [0002] There are restriction endonucleases inside cells that can destroy foreign DNA to resist the invasion of new viruses. [0003] Restriction enzymes cut DNA at specific sites, producing gene fragments that can be ligated in vitro. Restriction enzymes are usually accompanied by one or two modifying enzymes (methylases) that protect the cell's own DNA from damage by the restriction enzymes. The modifying enzymes recognize the same sites as the corresponding restriction enzymes, but methylate only one base in each strand instead of cutting the DNA strand. Restriction enzymes and methylases together constitute the restriction-modification (R-M) system. Type II enzymes specifically cleave the DNA stra...

AI Technical Summary

Problems solved by technology

[0009] The shortcomings of the existing software are: the sequence that can be input is limited, and the efficiency is prone to low when digested with multiple enzymes. The key is that the information of the sticky end and the sequence of each fragment cannot be preserved. What needs improvement most is that there is no suitable algorithm to help the research How large a range of fragments should the personnel choose is more suitable for the research in their own field

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