Automatic generation of pseudoknotted RNAs taxonomy.

ABSTRACT:

Background

The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as 16S rRNA. Most comparison methods and benchmarks in the literature focus on pseudoknot-free structures due to the difficulty of mapping pseudoknots in classical tree representations. Some approaches exist that permit to cluster pseudoknotted RNAs but there is not a general framework for evaluating their performance.

Results

We introduce an evaluation framework based on a similarity/dissimilarity measure obtained by a comparison method and agglomerative clustering. Their combination automatically partition a set of molecules into groups. To illustrate the fra

SUBMITTER: Quadrini M 

PROVIDER: S-EPMC10268371 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature