A method, system, equipment and medium for establishing a gene comparison table

Abstract

The invention discloses a method, system, device and storage medium for establishing a gene comparison table. The method includes the following steps: reading a subsequence of the first continuous length from a reference genome sequence as a seed, and determining the longest Read length; store multiple seeds in the buffer area in turn, use the first seed as the candidate seed, and judge whether the number of seeds in the buffer area reaches the threshold; in response to the number of seeds in the buffer area not reaching the threshold, judge the Whether the longest read length corresponding to the current seed stored in the cache is greater than the sum of the first length and the threshold; in response to the longest read length corresponding to the current seed being greater than the sum of the first length and the threshold, determine the hash value of the current seed Whether it is less than the hash value of the seed to be selected; and in response to the hash value of the current seed being less than the hash value of the seed to be selected, write the current seed into the gene comparison table, and update the current seed as the seed to be selected.

Description

technical field [0001] The present invention relates to the field of gene comparison, and more specifically refers to a method, system, computer equipment and readable medium for establishing a gene comparison table. Background technique [0002] The typical seed strand alignment program gene sequencing used by most whole gene comparisons, in order to quickly and accurately map the DNA subsequence to the reference genome, the general process is to collect the reference genome reference, and follow the K-mer or other algorithms. Shard into multiple seeds, and compile the seeds into a hash table. Then each sequence to be compared is divided, and its corresponding position on the table is retrieved by looking up the table. [0003] Now mainstream gene comparisons often use full-text indexes, such as suffix arrays or FM indexes. The advantage of this approach is that we can use seeds of any length, which helps to increase the uniqueness of the seeds and reduce unsuccessful ext...

AI Technical Summary

Problems solved by technology

Especially if multiple extension tables are created according to different seed lengths, the pressure on memory will increase exponentially

Moreover, the calculation speed of subsequent lookup tables will be very slow

If you simply read the reference seed at a certain interval, there will be many missing items, resulting in missing table item information and affecting the final accuracy

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