Method and system for quickly comparing whole genome annotation intervals

Abstract

The invention provides a method and a system for quickly comparing whole genome annotation intervals. The method comprises the following steps: S1, respectively obtaining a gene annotation interval A fragment coordinate set and a gene annotation interval B fragment coordinate set; s2, combining the coordinates of the fragment set A and the coordinates of the fragment set B to obtain a combined fragment set; s3, performing redundancy elimination operation and sorting operation on the combined fragment set; s4, calling a preset interval intersection function to calculate the intersection of all the annotation intervals in the merged fragment set in a single cycle; and S5, outputting a calculation result of the preset interval intersection function. According to the method, the intersection of different types of gene annotation intervals can be rapidly calculated, and compared with a traditional comparison method, the method is simple in implementation logic, small in calculation amount, accurate in judgment and beneficial to improvement of comparison efficiency.

Description

technical field [0001] The invention relates to the technical field of genome annotation, in particular to a method for rapidly comparing annotation intervals of the whole genome. Background technique [0002] At present, in the field of pests and diseases or rapid detection, it is often necessary to calculate the relationship between a large number of different annotation fragments in the whole genome. Since the number of genomes of organisms is usually very large, the number of annotation fragments involved is huge. Traditional calculation methods mainly include two , one is to establish a database index and compare it through a specific data structure. For example, in the paper "Building a Populus trichocarpa Gene Database and Realization of a Visualization Platform", it is disclosed that an index is established in a database visualization platform to search for genome fragments. The operation of the first method is relatively complicated, and for very large-scale data, i...

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Problems solved by technology

[0002] At present, in the field of pests and diseases or rapid detection, it is often necessary to calculate the relationship between a large number of different annotation fragments in the whole genome. Since the number of genomes of organisms is usually very large, the number of annotation fragments involved is huge. Traditional calculation methods mainly include two , one is to establish a database index and compare it through a specific data structure. For example, in the paper "Building a Populus trichocarpa Gene Database and Realization of a Visualization Platform", it is disclosed that an index is established in a database visualization platform to search for genome fragments. The operation of the first method is relatively complicated, and for very large-scale data, its processing speed will also be limited by the read and write speed of the hard disk; the other method is to search by comparing the intervals of genome annotations. For example, in the paper "Massive Genome Annotation Parallel Optimization and Implementation of Algorithms" discloses that most of the current gene function annotation software is written in scripting language, which analyzes the input sequence one by one, which is inefficient and takes a long time

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