This application is designed to make the process of drawing Gene Circuits easier and to scale. This project was created for and funded by the Mills Lab at UC-Davis.

To create a gene diagram you may either upload a genbank file or manually input genes to create a figure.

Max Length: The number of base pairs of the largest genome you will be comparing your figure too. This is in order to keep everything scaled relative to a maximum. For example if you have three species to compare, find the length of the longest and set Max Length to that one.

Block Height: Scale between 0 and 100 to determine how tall/thick each gene is

Arrow Length: Fixes length of arrows on blocks to be a percentage (0.00-100). Recommended to be 1 or below.

Range: For uploaded files, parse a certain range of the sequence for genes

After changing any of the above options the reload button must be hit.

Gene: Name of gene

Length: Length in base pairs of gene

Color: Color of block, either in english(red,green,blue,maroon,etc.) or hex (#ffffff)

Direction: Forward (right facing arrow) or backward (left facing arrow) for gene. Non Coding sets color to trasnparent.

Arrow Only: Checkbox to determine if the gene should only be a triangle and no rectangular portion.

-- Arrow length is as a percent of total SVG width

-- When parsing GenBank files overlaps of <10bp are set to 0. Anything >than 10bp overlap is deleted

-- Gene names from GenBank files are the predicted function by default. Will be set to the Locus_tag if no predicted function, and if neither name is set to "No Name"

-- I have no idea what would happen if you added a gene manually to an uploaded files diagram

Sincerely,

Samir Akre