XplasMap

Overview

XPlasMap is a DNA mapping program. It draws plasmid or linear DNA maps, showing features such as genes, multiple cloning sites, and restriction sites. The maps are highly customizable: colors, styles, position, and overall appearance of features can be changed. Fragments can be copied or cut, and inserted into different maps or turned into maps on their own (virtual cloning). FastA, text, and GenBank files can be imported directly, making maps of long and complex sequences (e.g. genomic sequences) quick and easy to prepare.

XPlasMap requires MacOS10.4 (Tiger). (Version 0.92, but not the latest v.0.96, is also available for MacOS10.3 (Panther).

XPlasMap is free (as in no cost) and can be redistributed as a complete package. I make no guarantees or warranties of any kind.

Downloads
Quick start
Examples
Release notes
License
Bug reports, feature requests, comments to iayork@iayork.com .
(Include "XPlasMap" in the subject to be sure my spam filters don't catch it.)

Quick start

• Start a new map from the Maps menu (⌘-N for circular, ⌘-Shift-N for linear map)
• Maps menu / Linear <> Circular to convert between circular and linear maps
• Draw linear DNA maps directly from GenBank files:
• Save a file to your computer, from GenBank in "GenBank (Full)" format
• Import (File menu / Import / from GenBank (.gb files))
• Choose which features listed in the GenBank (genes, mRNA, CDS, etc) you want to include on the map
• Draw maps directly from FastA or plain-text sequence files (File menu / Import / from FastA or Text)
• Directly identify restriction sites and open reading frames while importing sequences
• Set favourite restriction enzymes in Preferences
• Set ORF characteristics in Preferences
• Add new genes, new multiple cloning sites, new restriction sites, or new text from the Edit menu (or ⌘-G, ⌘- Shift-M, ⌘-R, or ⌘-T)
• Genes on linear (but not circular) maps can be shown as exon/intron diagrams, or as a single block
• Multiple cloning sites can be displayed in several styles
• Edit by double-clicking on the feature
• To edit a plasmid, click on the text in the center, or on the comment at the bottom (or "Edit plasmid info" from the Edit menu)
• Quick edits via contextual menu (control-click or right-click on the feature)
• Click and drag to move a feature
• Hold down ⌘ and drag to move a gene (click-and-drag moves the text of the gene only)
• Copy a fragment (⌘-C or Edit / Copy menu) for later pasting, or draw it as a linear fragment (Maps / New linear DNA or ⌘-Shift-N).
• Inserting a fragment (Edit menu): insert either a new, featureless section of DNA, a copied fragment from memory, or a linear DNA fragment from a saved file
• Cut a fragment (⌘-X or Edit menu) is the equivalent of collapsing out a region
• View as list (⌘-L or "View as list" in the Maps menu) for a sortable text summary of all DNA features
• Edit multiple features simultaneously using "View as list"
• Print maps (File / Print) or export as images (File / Export / to PNG or File / Export / to JPG) File / Print
• Set PNG or JPG resolution (high resolution/large files/slow export, or low resolution/small files/fast export) in Preferences

Release notes

• Version 0.96 (October 2007)
• Add comments and free-form text
• "Plasmid comment" is now free-form text (can be moved and edited)
• (Preference option) Common actions on a toolbar
• Improved print resolution
• Bugfixes:
• Clear Recent Files bug - fixed
• JPG and PNG exports use a large canvas with image only in one corner - fixed
• Copying in reverse doesn't reverse fragment - fixed
• Error on copying in reverse - fixed
• Print resolution too low - fixed
• Font preferences are not being honored - fixed
• Going from linear to circular, genes disappear - fixed
• Contextual menus not responding - fixed
• Show/Hide enzyme lost after save - fixed
• Genes with no name disrupt drawing - fixed
• Freeze in Cut Plasmid - fixed
• Hiccup if no Preference file - fixed
• Assorted other bugfixes and UI improvements
• Version 0.95 (July 2007)
• Automatic restriction enzyme mapping
• Automatic open reading frame identification
• Adjust resolution of exported PNG or JPG
• Scale adjust (Zoom in and out)
• Assorted bugfixes and UI improvements
• Version 0.9 (June 2007)
• Printing!
• Export to PNG or JPG
• Draw maps directly from GenBank or FastA files
• Genome maps showing exons
• Assorted bugfixes and UI improvements
• Version 0.8 (May 2007)
• Linear DNA maps
• Convert between linear and circular DNA maps
• Copy, save, and paste fragments from one map to another ("virtual cloning")
• Assorted bugfixes and UI improvements
• OS10.3.9-compatible version available
• Version 0.7 (April 2007)
• New formats for multiple cloning sites: boxed or text as well as arc
• New formats for genes: Reposition arcs, change thickness
• Assorted bugfixes and UI improvements
• Version 0.6 (March 2007)
• First general release

Info and license

XPlasMap is free for personal use.

Distribution of XPlasMap is allowed and encouraged, but only as a complete package (including any documentation, read-me, and copyright files). Use XPlasMap at your own risk. The author is not responsible for any damage, annoyance, or waste of time or materials resulting from the use of XPlasMap or incorrect information provided by XPlasMap.

XPlasMap was developed by Ian York (iayork@gmail.com), using Python and wx.Python:
http://www.python.org
http://www.wxPython.org

Additional modules used in XPlasMap: ElementTree (http://effbot.org/zone/element-index.htm)
BioPython (http://biopython.org/)
BioPython uses the eGenix mx extensions for Python

Thanks to Paul Tomblin and Clive Feather for geometry advice.

Please send feedback to iayork@panix.com/~iayork.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.