Release v1.0

Overview

We are pleased to announce the release of SERNAlign (Structural sEquence RNA secondary structure Alignment), version 1.0.

SERNAlign builds Structural Sequences from RNA secondary structures, including those with arbitrary pseudoknots, and computes the SERNA Distance by aligning two such sequences. A Structural Sequence is an abstraction of the arc diagram of an RNA secondary structure, in which nucleotide identities are ignored and arc topologies are represented as numerical sequences. Each RNA secondary structure corresponds to a unique Structural Sequence.

Assets included in this release

• SERNAlign-v1.0.jar: the core command-line tool that computes the SERNA Distance between two RNA secondary structures by aligning their Structural Sequences.
• SERNAlignWorkbench-v1.0.jar: a batch-processing command-line tool that takes a directory of RNA structures and performs all-vs-all comparisons using the SERNAlign algorithm. It outputs structure information and pairwise distance results, enabling large-scale analyses.
• README.v1.0.md: documentation including installation and usage instructions.

This release also provides the full source code under an open-source license.