AlignACE

AlignACE identifies conserved nucleic acid elements across sets of DNA sequences to locate regulatory motifs in upstream non-coding regions for studies of gene regulation.

Key Features:

• Pattern Recognition: Employs computational pattern-recognition algorithms to detect conserved sequence elements across multiple DNA sequences.
• Upstream Non-coding Region Analysis: Focuses searches on upstream non-coding regions of genes to locate candidate regulatory motifs.
• Regulatory Motif Identification: Identifies conserved motifs that are candidate transcription factor binding sites and other regulatory elements.
• Coregulated Gene Set Detection: Detects sets of mutually similar DNA elements to suggest groups of coregulated genes.
• Whole-genome mRNA Quantitation Integration: Integrates systematic whole-genome mRNA quantitation data to associate conserved elements with condition-responsive genes.

Scientific Applications:

• Galactose response in Saccharomyces cerevisiae: Identified the known Gal4 binding site and detected six of nine genes induced by galactose.
• Heat shock response: Revealed a cell-cycle activation motif mediating cell-cycle dependent activation and identified genes encoding nucleosomal proteins.
• Mating type regulation in Saccharomyces cerevisiae: Identified all four relevant DNA motifs and recovered most known alpha-specific genes.

Methodology:

Uses pattern-recognition algorithms to search upstream non-coding sequences for conserved DNA elements and incorporates systematic whole-genome mRNA quantitation to link conserved elements to responsive genes.