4SALE

4SALE aligns RNA sequences and their secondary structures synchronously to preserve structural information for comparative, evolutionary, and structural analyses.

Key Features:

• Synchronous Sequence and Structure Alignment: Aligns RNA primary sequences together with their secondary structures in a coordinated alignment.
• Manual Editing Capabilities: Enables manual synchronous editing of aligned sequences and their corresponding secondary structures.
• Optimal Starting Point for Analysis: Constructs an optimal and unique starting alignment for each RNA sequence and structure analysis.
• Visual Monitoring of Structural Aspects: Provides visualization of structural aspects during editing to monitor secondary-structure features.

Scientific Applications:

• RNA Function and Evolution Studies: Facilitates analyses aimed at understanding RNA function and evolutionary relationships by preserving structural context.
• Comparative Genomics: Supports comparative genomics investigations that require alignment of sequence and secondary-structure conservation.
• Evolutionary Studies: Enables evolutionary analyses using structure-aware alignments to assess conservation and divergence.
• Structural Biology Investigations: Assists structural biology studies that depend on accurate secondary-structure-aware alignments.

Methodology:

Performs synchronous alignment of RNA sequences and their secondary structures, allows manual synchronous editing of alignments, and constructs an optimal starting alignment for subsequent analyses.