GenePalette

GenePalette enables visualization and analysis of genome sequences to examine gene organization and cis-regulatory elements such as transcription factor binding sites.

Key Features:

• Cross-Platform Compatibility: Written in Java and compatible with Mac, PC, Unix, and Linux.
• Genome Visualization: Provides schematic graphical representations of genes and associated features, including color-coded elements and transcription factor binding sites (TFBSs).
• Sequence Annotation Mapping: Maps annotations directly onto nucleotide sequence views to show features in genomic context.
• Multi-scale Sequence Access: Provides access to raw sequence data at resolutions from kilobases down to individual nucleotides.
• Data Retrieval: Retrieves annotated sequences from public repositories including NCBI GenBank and Ensembl.
• Feature Positioning: Displays relative positions of genomic features with respect to introns and exons.

Scientific Applications:

• Cis-regulatory element analysis: Supports analysis of the organization and arrangement of cis-regulatory elements within genomic regions.
• Experimental design for regulatory regions: Facilitates design of wet-lab experiments targeting regulatory regions by visualizing annotations and feature positions.
• Gene regulation and expression studies: Enables investigation of gene regulation and expression through visualization of features relative to introns, exons, and gene structure.
• Annotated genome sequence examination: Allows examination and use of complete annotated genome sequences across multiple scales of resolution.

Methodology:

Retrieves annotated sequences from NCBI GenBank and Ensembl and renders schematic and nucleotide-resolution visualizations annotated with gene features including TFBSs; implemented in Java.