AGenDA

AGenDA predicts genes by comparative analysis of genomic sequences using phylogenetic footprinting to identify functionally conserved regions between evolutionarily related organisms such as humans and mice.

Key Features:

• Input Requirements: Accepts pairs of genomic sequences from closely related species, for example humans and mice, to enable comparative analysis.
• Alignment Algorithms: Employs the CHAOS and DIALIGN alignment algorithms to generate local sequence alignments for detection of conserved regions.
• Gene Prediction Methodology: Predicts genes by analyzing conserved splicing signals, start and stop codons, and other sequence conservation indicative of functional elements.
• Output Presentation: Produces graphical representations of alignments alongside predicted gene annotations.

Scientific Applications:

• Comparative gene prediction: Facilitates homology-based identification of genes conserved across species.
• Comparative genomics and evolutionary analysis: Supports detection of functionally conserved genomic regions to inform evolutionary relationships.
• Functional genomics and disease research: Aids investigation of genetic bases of phenotypic traits and disease mechanisms through conserved-region-based annotation.

Methodology:

Uses phylogenetic footprinting together with CHAOS and DIALIGN alignments to detect local sequence conservation and conserved splicing signals, start/stop codons for homology-based gene prediction.