NAPP

NAPP classifies coding and non-coding genomic sequences by their conservation patterns across multiple genomes to identify clusters enriched for functional non-coding elements such as small RNAs and cis-regulatory RNAs.

Key Features:

• Classification of coding and non-coding sequences: Classifies both coding and non-coding genomic sequences based on their conservation patterns across multiple genomes.
• Detection of functional non-coding clusters: Distinguishes clusters enriched for functional non-coding elements, particularly small RNAs and cis-regulatory RNAs.
• Structure-independent RNA discovery: Identifies previously undetected RNA genes or elements without relying on conserved RNA secondary structures.
• Clustering by phylogenetic occurrence profiles: Clusters sequences with similar occurrence profiles across genomes to group functionally related elements.
• Large-scale prokaryotic dataset: Applied to a collection of 949 bacterial species and 68 archaeal species to assess conservation patterns across prokaryotes.
• Improved analysis pipeline: Implements an improved pipeline for phylogenetic profile analysis.

Scientific Applications:

• Non-coding RNA discovery: Discovery and annotation of small RNAs and cis-regulatory RNAs across bacterial genomes.
• Comparative genomics of conserved elements: Comparative analysis of conserved coding and non-coding sequences across bacterial and archaeal genomes.
• Functional inference from conservation: Prioritization and functional analysis of candidate elements based on shared conservation and occurrence profiles.

Methodology:

Classification based on conservation patterns across multiple genomes, clustering sequences by phylogenetic occurrence profiles, and application of an improved pipeline to a dataset of 949 bacterial species and 68 archaeal species.