Mulan

Mulan performs local multiple DNA sequence alignments across finished and draft-quality genomic sequences to identify evolutionarily conserved transcription factor binding sites and localize functional coding and noncoding elements using comparative sequence conservation.

Key Features:

• Local multiple alignments: Computes local multiple DNA sequence alignments to detect conserved regions across genomes.
• Transcription factor binding site detection: Identifies evolutionarily conserved transcription factor binding sites within alignments.
• tba multisequence aligner: Integrates the tba multisequence aligner program for rapid identification of local sequence conservation.
• multiTF program: Uses the multiTF program to detect conserved transcription factor binding sites in aligned sequences.
• Cross-species comparison: Compares genomes ranging from closely related to distantly related organisms to identify conserved genetic elements over extended evolutionary periods.
• Rearrangement representation: Represents short- and large-scale genomic rearrangements through local multiple alignment computations.
• Duplication handling: Incorporates handling of duplications to improve reliability of reconstructing evolutionary events from genome sequence data.
• Genomic database integration: Integrates with the ERC Browser and UCSC Genome Browser for sequence data and with the GALA database to combine functional genome annotations with sequence conservation profiles.

Scientific Applications:

• Conserved regulatory element discovery: Identification of evolutionarily conserved transcription factor binding sites across diverse species.
• Comparative genomics of draft and finished genomes: Comparative analysis of finished and draft-quality genomic sequences to find conserved elements.
• Evolutionary event reconstruction: Reconstruction and analysis of genomic rearrangements and duplications across evolutionary time.
• Annotation of functional elements: Localization of functional coding and noncoding genomic elements via conservation signals.
• Phylogenetic inference from conservation: Use of sequence conservation and selective pressures to inform phylogenetic relationships.

Methodology:

Performs local multiple alignments using the tba multisequence aligner and scans alignments with the multiTF program to detect conserved transcription factor binding sites, with explicit handling of duplications and representation of genomic rearrangements.