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Quick Help Guide 1.0



Start by either clicking "Create a Plasmid", "Load a Plasmid", or "Enter Plasmid Seq."


Create a Plasmid		 Create a plasmid by entering the plasmid size in bp (ie. 6000 for a 6000bp plasmid) and a plasmid name. After entering both pieces of information click Start and the plasmid drawing program will begin.








Enter the plasmid size and name then click Start to being the drawing mode

Load a Plasmid		 You can load a previous plasmid drawn with eZ Plasmid Mapper. Simply copy and paste the saved code in its entirety into the text area and click Import. eZ Plasmid Mapper will store your plasmid information in XML format whenever you click Saved Plasmid while in the drawing mode.

Enter Plasmid Seq."
This mode is still in progress. You can the plasmid sequence (ie. AGTGTGT.......) into the text area the plasmid name. The program will create a plasmid with the appropriate size. You can also choose to have the program identify and mark Restriction Sites, and Genes. When your ready to start click Start near the bottom.


Find RE Sites		 Choose a RE set from the drop down menu. You can also add your own restriction sites by clicking Add RE and then entering the RE name and sequence. The program will search the plasmid sequence and mark all the RE sites found in the plasmid.

Find Regions		 This feature is still buggy and has its limitations. It will attempt to find the region in the plasmid allowing up to 2% of the total region size to be bp mismatches. It does NOT identify single/multiple bp deletions, insertions or frameshifts. It will search both 5' and 3' directions for the gene. The search algorithm is rather bulky so if too many regions are in the Search Library the program will stall/crash. You can add your own regions by clicking Add Sequence  and filling in the appropriate information. You can also preview the sequence by double clicking the cell, a small white box will popup. Click anywhere in the text area to close the box.














Double click the Double-Click text, and a small white box will appear showing you the sequence. You can scroll up and down to view the sequence in its entirety. Click anywhere in the TEXT region to close the box.


Drawing Mode allows you to make detailed/precise labels and features on your plasmid. After entering in your
initial plasmid details and clicking Start or Import (if loading), the program will take you to the drawing mode. Any label on the plasmid
can be moved by clicking on it and holding down the mouse button. Let go of the mouse to drop the label at its new position.

 







 

Restriction

Click on this to add a Restriction Site label to the plasmid map. A light blue box will appear asking you to enter the RE location in bp (ie. 553 for 553bp) and the RE Name. Click Close to cancel. After entering both pieces of information click Add and the RE name label will immediately begin following your mouse cursor. A line will also appear on the plasmid map marking the relative position of the RE site. Click anywhere on the plasmid map to place the label.

Gene and Color Box

Click on this to add a gene or region to the plasmid map. A light blue box will appear asking you to enter the following pieces of information.

Gene Start Enter the gene start location in bp (ie. 600 for 600bp)
Gene End
Enter the gene end location in bp (ie. 600 for 600bp)
Gene Name
 Enter the gene name
Rotation
Choose the gene rotation either clockwise or counterclockwise. This determines the location of the arrows visual.
Arrows
Uncheck this if you want to mark a bilateral region (ie. an ORF).


 

Export to jpg

Clicking here will allow you to export your eZ Plasmid as a *.jpg file. Depending on your browser a prompt should appear asking you to save a file called "ezPlasmidMap.jpg".


Save Plasmid

 Click here if you want to save your eZ Plasmid so that you can edit it at a later time. Please copy the code in its ENTIRETY. We suggest you save it by itself in a text file such as *.txt or *.doc
















Drawing Mode keeps track of all the added RE sites and regions in a grid on the right side of the screen. The Quick Help box
is allow shown in the bottom right hand corner. To remove a RE site or gene, simply select it from the grid and then click Remove Selected
Allowing Overlapping Genes
 Check this if you want to allow overlapping genes. Overlapped genes start closest to the center of the circle and expand out. If unchecked, then all genes will appear on the circular line marking the plasmid
Mark Gene Locations
 Only useful if you have Allow Overlapping Genes unchecked. It will mark the start and end locations of the gen on the plasmid map
Curve Gene Names
 A still in progress feature, but it will curve your gene name along the region. Once again only really usefull if you have Allow Overlapping Genes unchecked
Group RE Sites within 310 bp
 This will group all nearby RE sites within XX bp based on the size of the plasmid. You can still add/remove RE sites individually if this is checked.
Move RE lines with label
 This will allow you more flexibility in reposition the labels. Lines are automatically drawn to the RE site label. If you uncheck this, the line will remain FIXED, allowing you to move the RE name label freely