RNAlien

RNAlien constructs RNA family covariance models from a single input sequence through iterative homology search and structural alignment.

Key Features:

• Automated Covariance Model Construction: Iteratively identifies homologous sequences starting from one input sequence and builds covariance models capturing both sequence and secondary structure information.
• Structural Alignment and Consensus Structure: Generates multiple sequence structural alignments and consensus secondary structures for detected RNA family members.

Scientific Applications:

• Non-Coding RNA Family Annotation: Enables functional annotation and genome-wide identification of RNA family members using automatically generated covariance models.

Methodology:

RNAlien performs iterative homology searches to collect related sequences, constructs structural alignments, derives consensus secondary structures, and automatically builds covariance models for RNA family detection and classification.