YASS

YASS performs local alignment searches to identify regions of similarity and conserved motifs in nucleic acid sequences (DNA and RNA) from FASTA or plain text inputs.

Key Features:

• Local alignment search: Generates local pairwise alignments to detect regions of similarity between sequences.
• Input formats: Analyzes sequences provided in FASTA or plain text formats.
• Transition-constrained seeds: Employs transition-constrained seeds as a core filtering strategy.
• Flexible hit criterion: Integrates a flexible hit criterion to identify groups of seeds likely to produce significant alignments.
• Sensitivity and specificity: Uses the combination of transition-constrained seeds and flexible hit criteria to enhance both sensitivity and specificity of detection.

Scientific Applications:

• Detection of local similarity: Identifies regions of local sequence similarity between homologous DNA and RNA sequences.
• Conserved motif identification: Pinpoints conserved motifs within homologous sequences using seed-based filtering.
• Pairwise sequence analysis: Produces local pairwise alignments for comparative analysis of nucleic acid sequences.

Methodology:

Analyzes FASTA or plain text sequences, applies transition-constrained seeds as a filtering algorithm combined with a flexible hit criterion to group seeds, and generates local pairwise alignments.