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Convert embl to circular map pdf

This page is designed to accept one or more annotated embl format files plus a fasta sequence file, and output a nice looking circular feature map in pdf format.

This converter is based on the circular_diagram.pl perl script written by the Sanger Institute.

Instructions:

Select at least one embl file and one fasta sequence file, then select your options. Each embl file of features will be displayed as an concentric ring in the final pdf.
Reasonable defaults are already entered, but feel free to make changes
and see how it changes the result. When you are ready, click "Make PDF!"

Note that one unit of height or width = 1/72 of an inch.

Choose Files:

Please select a fasta format sequence file to upload. Must be fasta format.


Please select an embl format file to upload. Must be embl format.

Radius:
Radius indicates where on the circle features from this embl file should be drawn. 0 is the center 100 is the edge of the circle.

Feature Height:
Feature Height indicates the thickness of the features drawn in that circle.


Ready?


Additional Optional Files

Optionally, please select a second embl format file to upload.

Radius:
Feature Height:


Optionally, please select a third embl format file to upload.

Radius:
Feature Height:


Optionally, please select a fourth embl format file to upload.

Radius:
Feature Height:


Optional GC Content Calculation

Show GC ratio ring?:
What it is: If "yes" is selected, the GC ratio of the sequence will be calculated and displayed in a ring.

GC Window size:
What it is: The number of bases over which a running average GC is calculated.

GC Step Size:
What it is: The "resolution" of the GC content calculation. Higher numbers will have a smoother appearence.

Radius:
Feature Height:


Optional GC Skew Calculation

Show GC Skew ring?:
What it is: If "yes" is selected, the GC skew of the sequence will be calculated and displayed in a ring.

GC Skew Window size:
What it is: The number of bases over which a running average GC skew is calculated.

GC Skew Step Size:
What it is: The "resolution" of the GC Skew calculation. Higher numbers will have a smoother appearence.

Radius:
Feature Height:


More Available Options


Page Width:
What it is: the width of each page. The default 594 = 8.25 inch

Page Height:
What it is: the height of each page. The default 792 = 11 inch

Scale Font Size:
What it is: the size of the font. Not the same scale as you are used to.

Label Distance:
What it is: the distance between the scale line/circle and the centre of the scale labels

Scale Label Distance:
What it is: the distance between the scale numbers in bases. Enter "0" for no labels.

Scale Tick Mark Distance:
What it is: the distance between the scale tick marks in bases. Enter "0" for no labels.

Scale Tick Mark Thickness:
What it is: the thickness ofthe scale tick marks

Scale Tick Mark Height:
What it is: the height ofthe scale tick marks

Minimum Feature Width:
What it is: the minimum width of a feature in bases

Draw Direction
What it is: which direction to draw the figure

End Gap:
What it is: the gap (in bases) between the last base of the sequence and the first. This option exists to allow non-circular genomes to be drawn sensibly

Show Command Line?
What it is: Display in the browser all the command line options used to generate the pdf

Ready?

Details on this software are hard to find, but we found mention of this script here and downloaded it from here.