Approximate search for known gene clusters in new genomes using PQ-trees.

ABSTRACT: Gene clusters are groups of genes that are co-locally conserved across various genomes, not necessarily in the same order. Their discovery and analysis is valuable in tasks such as gene annotation and prediction of gene interactions, and in the study of genome organization and evolution. The discovery of conserved gene clusters in a given set of genomes is a well studied problem, but with the rapid sequencing of prokaryotic genomes a new problem is inspired. Namely, given an already known gene cluster that was discovered and studied in one genomic dataset, to identify all the instances of the gene cluster in a given new genomic sequence. Thus, we define a new problem in comparative genomics, denoted PQ-TREE SEARCH that takes as input a PQ-tree T representing the known gene orders of a gene

SUBMITTER: Zimerman GR 

PROVIDER: S-EPMC8272295 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature