RNAlien

RNAlien is a computational tool that streamlines the process of annotating non-coding RNA (ncRNA) sequences by determining their homology and thereby inferring functionality and family membership. This tool addresses the challenge of identifying the function of ncRNAs, which traditionally relies on costly and time-consuming wet lab experiments. RNAlien offers a computational alternative, leveraging covariance models to assign novel RNA sequences to known RNA families.

The unique aspect of RNAlien is its ability to start with a single input sequence and iteratively collect potential family member sequences through multiple rounds of homology search. This process allows for fully automating RNA family models based on the gathered sequences, a significant advancement because constructing such models requires numerous known examples of the family and involves experts manually editing RNA alignment and consensus structure.

RNAlien has been tested on a subset of the Rfam RNA family database, demonstrating its capability to produce models that can serve as starting points for constructing models with sensitivity and specificity comparable to manually curated ones found in Rfam. This ability makes RNAlien an invaluable resource for researchers looking to annotate newly sequenced genomes computationally, facilitating a more efficient and cost-effective approach to understanding the roles and relationships of ncRNAs within biological systems.