Genome restriction map splicing method and system

Abstract

The invention relates to the field of genomic sequence splicing in the field of molecular biology, and provides a genome restriction map splicing method and system. The method includes the steps of preprocessing gene sequence molecules in the genome restriction map, obtaining new gene sequence molecules, and cutting the new gene sequence molecules into FLES segments, wherein the FLES segments are gene segments which have the fixed total segment lengths and do not need to have the same restriction locus number; clustering the FLES segments to form a representative FLES set, and conducting error correction on the gene sequence molecules according to the representative FLES set; establishing an FLES map according to the FLES set and the gene sequence molecules where error correction is conducted, conducting route search on the FLES map, obtaining the Hamilton route of the FLES map to serve as the restriction locus sequence of a genome, and completing splicing of the genome restriction map. By means of the method and the system, the restriction locus map of the genome can be rapidly and accurately established.

Description

technical field [0001] The invention relates to the field of genome sequence splicing in the field of molecular biology, in particular to a method and system for splicing genome restriction map. Background technique [0002] The genome contains the most basic genetic information of an organism, which determines the biological characteristics of the species, guides the operation of life functions and development processes; and guides the synthesis of important compounds in cells (such as proteins, RNA, etc.). [0003] The genome sequence is a double helix structure formed by deoxyribonucleotides (adenine A, guanine G, thymine T, and cytosine C) connected to each other by 3'-5'-phosphodiester bonds in a certain order. The so-called genome sequencing refers to obtaining the sequence information of the deoxyribonucleotides of the genome. With the development of genome sequencing technology, the genomes of more and more species have been determined. [0004] The development of ...

AI Technical Summary

Problems solved by technology

The second-generation sequencing technology has gradually become the mainstream sequencing technology due to its high-throughput and low-cost characteristics. However, both Sanger sequencing and second-generation sequencing technologies have limited sequencing lengths, and it is difficult to span the genome. Some longer repeats (repeated sequences) in the genome, where "repeat" refers to sequences that appear more than once on the genome, the existence of repeats makes it difficult to directly restore the complete genome through next-generation sequencing data splicing, however Research such as structural variant detection relies on the complete sequence information of the genome, so higher requirements are placed on sequencing technology

Anantharaman, T.S., B.Mishra, and D.C.Schwartz, Genomics via optical mapping. II: Ordered restriction maps. J Comput Biol, 1997.4(2): p.91-118. In this paper, the Bayesian method is used to predict the occurrence of loci The probabilistic model is used to assemble the map molecules. The shortcomings of this method mainly include how to set the prior of the Bayes model and the high computational complexity.

Anantharaman, T., B. Mishra, and D. Schwartz, Genomics via optical mapping. III: Contiging genomic DNA. Proc Int Conf Intell Syst Mol Biol, 1999: p.18-27. Using the idea of ​​sequence alignment to construct restriction enzymes Site map, the algorithm has shortcomings: (1) it is very time-consuming to find the optimal sequence alignment, (2) some heuristic strategies are introduced to reduce the time complexity, but the accuracy is lost

Images