A method for identifying horizontally transferred genes based on locality-sensitive hashing

Abstract

The invention discloses a method for identifying horizontally transferred genes based on local sensitive hashing, which includes the following steps: step 1, cutting the whole genome data into N fragments with the same bp number according to the set step size; step 2, cutting each fragment Carry out K-word processing; Step 3, count the term frequency of the K-word in each segment and standardize; Step 4, build m hash function families, calculate the m hash values ​​of each segment; Step 5, for each The m hash values ​​​​of the gene fragment are processed in rows, and the hash value in the row of the fragment is compared with the hash value in the row of the whole genome. When all the hash values ​​​​in at least one row are equal, the fragment is considered to be the same as the whole genome. Similar; otherwise, it is predicted that horizontal gene transfer will occur; step 6, calculate the Euclidean distance between the candidate fragments in the similar set and the m hash values ​​of the whole genome if it is greater than the set threshold, then horizontal gene transfer will occur. The invention helps to reduce computer resource usage and improve prediction calculation efficiency.

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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