Gene sequence comparison method and system, and related assembly

Abstract

The invention discloses a gene sequence comparison method. The method comprises steps that a to-be-compared sequence and a reference sequence are determined, and a pointer table and a candidate comparison position table are determined according to the reference sequence; a seed sequence of a preset length is extracted from the to-be-compared sequence, and an index value of the seed sequence is determined; the pointer table and the candidate comparison position table are queried according to the index value of the seed sequence; whether the position information corresponding to the seed sequence exists in the reference sequence is determined; if yes, the seed sequence is used as a to-be-extended sequence, according to the position information, on the basis of the reference sequence, the to-be-extended sequence is extended to obtain an intermediate sequence, and the intermediate sequence and the to-be-compared sequence are compared to obtain the gene sequence comparison result. The method is advantaged in that the storage space of the table storing the reference sequence index value can be reduced, and the gene sequence comparison rate can be increased. The invention further discloses a gene sequence comparison system, a computer readable storage medium and an electronic device. The advantages are realized.

Description

technical field [0001] The invention relates to the interdisciplinary field of computer technology and biological gene technology, in particular to a method and system for gene sequence comparison, an electronic device and a computer-readable storage medium. Background technique [0002] The strategy of gene sequence alignment usually mainly includes two stages of seed (seed sequence) search and seed expansion. The main step of the seed search stage is to search for a subsequence of a certain length on the read (sequence to be compared) that can completely and accurately match the reference sequence, that is, the seed (seed sequence). In the extension stage, the found seed is extended on the seed sequence of the reference sequence. Finally, the best alignment result is selected according to the scores on each seed sequence. [0003] In the prior art, in order to quickly and accurately match the seed to the reference sequence, the reference sequence can be pre-indexed, and ...

AI Technical Summary

Problems solved by technology

However, since the index table needs to be established bit by bit on the entire reference sequence, the required storage space is very huge

Therefore, use FPGA (Field-Programmable Gate Array, that is, field programmable gate array) to compare the access of the index table according to the index value, and the access rate of the random access is low.

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