Alfresco

Alfresco provides integrated visualization and aggregation of results from external analysis programs to support comparative genome sequence analysis and the identification of homologous protein-coding and regulatory regions.

Key Features:

• Integrated visualization: Displays and aggregates results from multiple external analysis programs, including database searching, gene prediction, repeat masking, and alignment tools.
• Pairwise comparative handling: Operates on pairs of putatively homologous sequences from different species for direct sequence comparison.
• Comparative analysis support: Enables identification of protein-coding and regulatory regions through cross-species homology comparison.
• Functional domain identification: Visualizes outputs from diverse computational tools to pinpoint corresponding functional sequence domains between species.

Scientific Applications:

• Gene prediction and annotation: Assists in predicting genes and annotating genomic regions by comparing homologous sequences across species.
• Protein homology studies: Identifies conserved protein-coding regions indicative of shared biological function.
• Regulatory sequence analysis: Supports prediction and analysis of regulatory sequences via visualization of homologous genomic regions.
• Orthologous locus analysis (human–mouse UTY): Applied to analysis of unannotated orthologous genomic sequences such as parts of the UTY locus between human and mouse.

Methodology:

Alfresco handles pairs of putatively homologous sequences from different species and aggregates outputs from external programs (database searching, gene prediction, repeat masking, alignment tools) into a unified visualization to facilitate comparative analysis and identification of homologous regions and functional domains; the implementation is Java-based.