System and method for base sequence alignment

Abstract

Provided are a system and method for sequence alignment. The system for sequence alignment includes an exact matching module configured to perform exact matching of an input read to a reference sequence, a secondary matching module configured to map the read to the reference sequence in consideration of mismatches between the read and the reference sequence when the read does not exactly match the reference sequence, and a global alignment module configured to perform global alignment operation of the read with the reference sequence when the read is not mapped to the reference sequence by the secondary matching module.

Description

technical field [0001] An embodiment of the present invention relates to a technique for analyzing the base sequence of a genome. Background technique [0002] Next Generation Sequencing (NGS: Next Generation Sequencing), which is used to produce large-capacity short sequences, is rapidly replacing the traditional Sanger (Sanger) sequencing method because of its low cost and fast data production method. Also, various NGS sequence alignment programs have been developed with emphasis on accuracy. [0003] The first step of sequence recombination is to map the short fragment (read) to the exact position of the reference sequence by base sequence alignment (alignment) algorithm. For this reason, a common existing base sequence alignment algorithm first maps a predetermined length of seed (seed) selected from a short fragment to a reference sequence, and then performs global alignment (Global Alignment) on the remaining short fragments at the mapped position. ). [0004] For s...

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Problems solved by technology

However, the complexity of global alignment is O(N 2 ), its execution time is very long, so if according to the prior art, the outstanding problem is that the base sequence alignment time increases geometrically with the increase of candidate positions

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