Encoding method for rapidly encoding gene character sequence into binary sequence

Abstract

The invention discloses an encoding method for rapidly encoding a gene character sequence into a binary sequence. The encoding method comprises the steps of: 1, taking out a specified number of character strings from a gene character sequence to be encoded and using the taken character strings as currently processed character strings; 2, shifting binary codes of the currently processed character strings right by one bit; 3, carrying out a data AND-operation on each character in the currently processed character string shifted right by one bit and 0x3; 4, respectively extracting and assembling two lowest bits in each character in a result after the data AND-operation to obtain a compact code binary sequence corresponding to the currently processed character strings; and 5, judging whether processing on the gene character sequence to be encoded is completed, skipping to execute the step 1 if processing is not completed, otherwise ending and exiting. The encoding method has the advantages of high encoding compression efficiency, high encoding speed, high encoding efficiency, no requirement for carrying out case change, flexible implementing mode and wide application range.

Description

technical field [0001] The invention relates to gene sequencing technology, in particular to a coding method for rapidly coding a gene character sequence into a binary sequence. Background technique [0002] With the development of gene sequencing technology, the price of sequencing has dropped exponentially, even faster than Moore's Law. With the large amount of sequencing data that comes with it, although the Internet and hardware continue to update and develop, the compression, storage, and transmission of the massive data generated by sequencing still pose great challenges. Both the DNA genome sequence and the sequencing sequence are composed of ATCG four bases. The encoding of A, T, C, and G is very important in data compression. The usual practice is as follows: due to the mixed case of characters, the character case can be unified Convert all to uppercase or lowercase (or directly judge without converting uppercase and lowercase, and the judgment situation increases ...

AI Technical Summary

Problems solved by technology

Since such encoding is performed word by word, it is very time-consuming for GB or even TB of DNA data, and it is very important to improve the encoding speed and efficiency

Therefore, the existing encoding method of encoding the gene character sequence into a binary sequence has the problems of slow speed and low efficiency when encoding the massive data generated by DNA sequencing.

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