Horizontal transfer gene recognition method based on locally sensitive hashing

Abstract

The invention discloses a horizontal transfer gene recognition method based on locally sensitive hashing. The horizontal transfer gene recognition method comprises the following steps: step 1, cuttingthe whole genome data into N fragments with the same bp number according to the set step length; step 2, performing K-word processing on each fragment; step 3, counting the K-word frequency of each fragment and performing standardization; step 4, constructing m hash function families and calculating m hash values of each fragment; step 5, dividing the m hash values of each gene fragment into lines, comparing the hash values in the lines of the fragment with the hash values in the lines of the whole genome and considering that the fragment is similar to the whole genome when all the hash values of at least line are equal; otherwise, predicting that horizontal gene transfer occurs; and step 6, calculating the Euclidean distance between the candidate fragments in the similar sets and the m hash value of the whole genome and indicating occurrence of horizontal gene transfer when the Euclidean distance is greater than the set threshold value. The computer use resources can be reduced and the prediction computing efficiency can be improved.

Description

technical field [0001] The invention relates to the field of biological information processing, in particular to a method for identifying horizontally transferred genes based on local sensitive hashing. Background technique [0002] Horizontal gene transfer (HGT) refers to the information exchange of genetic material between unicellular and (or) multicellular organisms in a horizontal manner, that is, the process in which organisms obtain genetic material from individuals other than their parents. An important process that promotes the evolution of species. Horizontal gene transfer can occur between different species (horizontal gene transfer between species) or between the same species (horizontal gene transfer within species). It breaks down the boundaries of kinship, complicating the possibility of gene flow. [0003] With the completion of the genome sequencing of humans and other organisms, it has been found that there are a large number of homologous genes in the gen...

AI Technical Summary

Problems solved by technology

But phylogenetic methods rely heavily on the accuracy of the input inherent genes and species trees, which can be challenging for gene tree and species tree construction

Even if there are no errors in the input tree, contradictory phylogenies may be the result of evolutionary processes other than HGT (such as duplications and losses), causing these methods to incorrectly infer HGT

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