diagram_tutorial.pdf

The Nugget

Genome Neighborhood Diagrams provide a visualization of the relationships between genes in a genome, with the "query" ID at the center in red and colored arrows representing different gene families. The tool allows for detailed exploration and manipulation of these diagrams.

Key quotes

"Each arrow is colored according to the Pfam that it belongs to."
"Loading and Filtering: Diagrams can contain thousands of proteins, but only 20 diagrams are shown initially."
"The SVG files downloaded from the Viewer contains arrows and diagrams that can be manipulated in an editor after the fact, without compromising the integrity of the image."
"Inkscape is a free vector graphics editor that runs on Windows, Mac OS X, and Linux, and is available at https://inkscape.org/en/."
"To export to PNG, go to File → Export PNG Image; this opens a window where export parameters can be edited."

The "query" ID is the central protein in the diagram, always colored red and pointing in the "Forward" direction (5’ to 3’).
Arrows in the diagrams are colored based on the Pfam they belong to, with some arrows having multiple colors representing fusion proteins.
The tool allows users to explore diagrams from BLAST runs, protein lists, or SSNs, with options to view specific proteins or clusters.
Filters can be applied to highlight specific Pfams, and the genome window parameter determines the number of neighboring genes shown.
Tools like downloading original diagrams, saving as SVG, and highlighting proteins with specific Pfams enhance the user experience.

Editing SVG Files: Inkscape allows users to open and edit SVG files downloaded from the Genome Neighborhood Diagram viewer tool.
Manipulating Diagrams: Diagrams in Inkscape can be manipulated by deleting, shifting, and reordering elements to customize the visualization.
Exporting Images: Inkscape enables the export of edited diagrams to various formats like PNG, PDF, EPS, and more, with options to adjust parameters like DPI for different purposes.

💡 Visualize Relationships: Genome Neighborhood Diagrams help visualize gene relationships in genomes, with colored arrows indicating gene families.
🎨 Edit with Ease: Inkscape enables easy editing of SVG files, allowing users to customize diagrams by deleting, shifting, and aligning elements.
🖼️ Export Like a Pro: When exporting diagrams from Inkscape, consider the purpose of the image to adjust parameters like DPI for optimal quality.
🧬 Highlight Pfams: Utilize the Pfam Filtering tool to highlight proteins with specific Pfams in the Genome Neighborhood Diagrams tool.

This summary contains AI-generated information and may have important inaccuracies or omissions.