ACES

ACES analyzes sequence conservation across multiple reference genomes to identify conserved regions of interest such as enhancers, promoters, and exons.

Key Features:

• Automated Querying: Accepts a query sequence and queries it against multiple reference genomes using corresponding FASTA files.
• BLAST Hits Generation: Runs BLAST searches to generate sequence similarity hits for the query across each reference genome.
• Multiple Sequence Alignment: Produces a multiple sequence alignment file aggregating homologous sequences identified across genomes.
• Graphical Fragment Assembly: Generates a graphical fragment assembly file representing how the query aligns with genomic fragments across genomes.
• Phylogenetic Tree Construction: Constructs a phylogenetic tree file to represent evolutionary relationships among identified homologs.

Scientific Applications:

• Evolutionary biology: Assesses conservation patterns and evolutionary relationships among species using alignments and phylogenetic trees.
• Comparative genomics: Identifies conserved regulatory elements and coding sequences across multiple reference genomes.
• Regulatory element analysis: Detects conserved enhancers and promoters by comparing query sequences across species.
• Coding sequence conservation: Evaluates exon conservation to inform hypotheses about functional importance of coding regions.

Methodology:

Queries sequences against reference genomes using FASTA files, performs BLAST to obtain hits, produces multiple sequence alignments, generates graphical fragment assembly files, and constructs phylogenetic tree files.