Software.ncrna.org

Software.ncrna.org performs structural analysis of non-coding RNA (ncRNA) sequences to provide secondary-structure-aware alignments and motif discovery for studies of ncRNA function and evolution.

Key Features:

• Structural Multiple Sequence Alignments: Aligns multiple ncRNA sequences using predicted or known secondary structures to identify conserved structural motifs and evolutionary relationships.
• Structural Pairwise Sequence Alignments: Performs pairwise alignments that incorporate secondary-structure information for more accurate sequence comparisons than sequence-only methods.
• Structural Motif Finding: Identifies and analyzes structural motifs within ncRNA sequences to characterize functional elements not apparent from primary sequence alone.

Scientific Applications:

• Functional Annotation: Uses detected structural motifs to infer potential functions of unknown ncRNAs.
• Comparative Genomics: Employs structural alignments to compare ncRNA sequences across species and assess conservation and divergence.
• Evolutionary Studies: Highlights conserved structural features among ncRNAs to elucidate evolutionary relationships.

Methodology:

Algorithms integrate secondary-structure information with nucleotide sequence data during alignment and motif discovery.