PAL

PAL computes optimal structural alignments between RNA sequences and genomic substrings to identify and analyze pseudoknotted non-coding RNAs by leveraging sequence conservation and secondary-structure information.

Key Features:

• Optimal Structural Alignment: Implements an algorithm for computing optimal structural alignments between RNA sequences and genomic substrings, accommodating pseudoknotted secondary structures.
• Discovery of Novel ncRNAs: Scans entire genomes to detect homologous pseudoknotted non-coding RNAs using conserved sequence and structural motifs.
• Secondary Structure Inference: Infers secondary structures of target sequences that align with known RNA motifs, including pseudoknots.

Scientific Applications:

• Identification of Homologous Pseudoknotted ncRNAs: Detects conserved pseudoknot structures to identify homologs indicative of functional similarity across species or viral strains.
• Genome-wide Searches: Performs genome-scale scanning for pseudoknotted ncRNAs in organisms including viruses and mouse genomes.
• Validation through Controlled Tests: Exhibits high sensitivity and specificity in controlled tests for detecting true homologs.

Methodology:

Uses an algorithm that integrates primary sequence data with secondary-structure conservation to compute optimal structural alignments, scan genomic substrings for conserved structural motifs (including pseudoknots), and infer secondary structures of aligned target sequences.