Short sequence mapping method and system

A mapping method and short-sequence technology, applied in the field of genetic engineering, can solve problems such as long processing time, low efficiency, and inability to meet short-sequence assembly requirements, and achieve short processing time and high efficiency

Inactive Publication Date: 2009-05-13
SHENZHEN HUADA GENE INST
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Problems solved by technology

[0004] The purpose of the embodiment of the present invention is to provide a short sequence mapping method, aiming to solve the problem that the existing short sequence comparison software has long processing time and low efficiency when processing the alignment between contig and short sequences, and cannot well meet short sequence alignment requirements. Problems with Requirements in Sequence Assembly

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[0017] In order to make the object, technical solution and advantages of the present invention clearer, the present invention will be further described in detail below in conjunction with the accompanying drawings and embodiments. It should be understood that the specific embodiments described here are only used to explain the present invention, not to limit the present invention.

[0018] In the embodiment of the present invention, by sorting the sequencing sequence according to the base value of the prefix short string of a preset length, and cutting the contig into short strings of a preset length base by base, the short strings cut in the contig are sequentially The base value searches for the corresponding sequencing sequence in the sorted sequencing sequence, and establishes a mapping relationship.

[0019] figure 1 The implementation flow of the short sequence mapping method provided by the embodiment of the present invention is shown, and the details are as follows: ...

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Abstract

The invention is applicable to the technical field of gene engineering, and provides a method for mapping a short sequence and a system thereof. The method comprises the following steps: ordering an order-checking sequence according to base values of prefixed short strings with predetermined length; cutting each base of a contig to a short string with the predetermined length; searching a corresponding order-checking sequence in an ordered order-checking sequence in sequence according to the base value of the cut short string in the contig so as to establish a mapping relation. In the invention, the method for mapping the short sequence used in a short sequence assembly is realized by ordering the order-checking sequence according to the base values of the prefixed short strings with the predetermined length, cutting each base of the contig to the short string with the predetermined length and searching the corresponding order-checking sequence in the ordered order-checking sequence in sequence according to the base value of the cut short string in the contig so as to establish the mapping relation. Therefore, the method has short treatment time and high efficiency.

Description

technical field [0001] The invention belongs to the technical field of genetic engineering, and in particular relates to a short sequence mapping method and system. Background technique [0002] The assembly of short sequences of large genomes faces memory challenges. In order to reduce the memory usage of building de Bruijn graphs, the assembly software can not record the correspondence between sequencing sequences and sequence fragment contigs (contig) in memory, but only in contig After assembly, map the correct sequencing sequence to the contig. There are two types of existing short sequence alignment software, one uses a combination index structure of fixed short strings, and the other uses a suffix tree-like index structure. Existing short sequence alignment software can map short sequences to contig within two mismatches, but since the starting point of these alignment software is not the alignment between contig and sequences participating in splicing, in particular...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/00C12Q1/68G06F19/22
Inventor 阮珏朱红梅李瑞强王俊杨焕明汪建
Owner SHENZHEN HUADA GENE INST
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