PanForest: predicting genes in genomes using random forests.

ABSTRACT:

Motivation

The presence or absence of some genes in a genome can influence whether other genes are likely to be present or absent. Understanding these gene co-occurrence and avoidance patterns reveals fundamental principles of genome organization, with applications ranging from evolutionary reconstruction to rational design of synthetic genomes.

Results

PanForest, presented here, uses random forest classifiers to predict the presence and absence of genes in genomes from the set of other genes present. Performance statistics output by PanForest reveal how predictable each gene's presence or absence is, based on the presence or absence of other genes in the genome. Further, PanForest produces statistics indicating the importance of each gene in predicting the presence or absen

SUBMITTER: Beavan AJS 

PROVIDER: S-EPMC12857576 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature