A method, system and related components for gene sequence comparison

Abstract

The present application discloses a method for gene sequence comparison, the method includes determining the sequence to be compared and the reference sequence, and determining a pointer table and a candidate comparison position table according to the reference sequence; extracting a seed sequence of a preset length from the sequence to be compared , and determine the index value of the seed sequence; according to the index value of the seed sequence, query the pointer table and the candidate comparison position table to judge whether there is position information corresponding to the seed sequence in the reference sequence; if so, use the seed sequence as the sequence to be expanded, and according to the position information Based on the reference sequence, the extended sequence is extended to obtain the intermediate sequence, and the intermediate sequence is compared with the sequence to be compared to obtain the gene sequence alignment result. The method can reduce the storage space of the table for storing reference sequence index values, and improve the gene sequence comparison rate. The application also discloses a gene sequence comparison system, a computer-readable storage medium and an electronic device, which have the above beneficial effects.

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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