Plasmid map drawing, restriction site mapping, and virtual cloning
CloneMap provides a complete solution for fast and easy plasmid map drawing,restriction site mapping, and virtural cloning. High-quality plasmid maps can be created with or without DNA sequences. Map features can be added by restriction site searching, feature table parsing, or easy, interactive manual entry. Restriction sites can be displayed on the map using predefined enzyme filters, or reported as text files summarizing sites together with DNA sequences. Common DNA sequence manipulations such as translation, open reading frame identification and display, and sequence conversion are provided. Free form graphic drawing objects, floating text, and Windows metafile can be added to the map to enhance map presentation. Map fragments can be inserted or deleted to generate related maps, with concomitant changes in the underlying DNA sequences.
CloneMap environment
Feature highlights
Object-based drawing environment. Every map element can be moved/adjusted.
CloneMap combines the power of DNA sequence manipulation and the fexibility of an object-oriented drawing environment, enabling you to produce plasmid maps exactly as what you want them to be.
Circular and linear plasmid maps created with or without DNA sequence.
CloneMap constructs both circular and linear maps, and converts easily between them. Map features can be defined in the absence of DNA sequences, allowing maps to be made from only structural information of the plasmid molecules.
However, if you have DNA sequence available, either in a disk file or in the clipboard,CloneMap can create a map instantly for you to use as a starting point.
Easy and interactive entry of restriction sites and regions.
CloneMap provides visual feedback to show the position of the mouse pointer, making interactive entry of map features fast and easy.
Restriction site mapping and restriction site reporting.
Restriction sites in a DNA sequence can be selectively displayed on the map in graphic form, or summarized in text form, with many flexible options.
Display sequence and map in the same window.
DNA sequence of a map can be viewed in the same map window, helpful for coordinating map features with their underlying sequences.
Import GenBank/EMBL feature tables.
Feature tables in GenBank/EMBL files are converted to map features, so you can visualize important pre-existing sequence information as part of the map. CloneMap recognizes 'joined' and 'complemented' CDS, which are useful for drawing exons in many eukaryotic genes.
Powerful and convenient enzyme filters.
Flexible enzyme filters are provided to make maping sequences with a selected set of enzymes as easy as a mouse click.
Translation.
DNA sequences can be translated into any or all six reading frames, and resulting protein sequences can be edited and exported.
Identification and graphic display of open reading frames.
Open reading frames in any or all six reading frames can be identified and displayed on the graphic map.
Cut/copy/paste features between maps.
Map features can be moved between maps, allowing speedy creation of map features from related maps.
Insert and delete plasmid fragments.
Map fragments can be inserted or deleted, with automatic update of map features. This simulates the cloning process, and allows you to generate maps quickly from othe rmaps.
Automatic linkage between maps and sequences.
Changes in the map during insertion or deletion are automatically updated at the DNA sequence level.
Add graphic drawing objects and metafiles to enhance the map.
CloneMap lets you create drawing objects such as lines and arrows to add illustrations to your map. You can also import metafiles or bitmap images and mix them with the map.
Complete text editing tool for map annotation.
CloneMap supports text editing both in the map window and in the text window, giving you flexibility for annotating maps. The text editor allows you to open and edit any text files, including restriction site report generated in the program.
Export maps as Windows metafiles.
Maps can be save as CloneMap native files for further editing. They can also be exported as Windows metafiles to be used in other drawing or word-processing programs.
Toolbar for easy access of common commands.
Many commonly used commands are also available from the toolbar, increasing your work efficiency.
Easy to use, context-sensitive on-line help and printed manual. Clean and logical interface design makes CloneMap extremely easy to use. In addition, CloneMap comes with a printed manual and comprehensive, context-sensitive on-line help.
Tools in the toolbar
This summary of tools illustrates some functions available in CloneMap. More tools can be accessed from menu commands.
Features on a linear map
In this exmaple, exons are converted from GenBank feature tables, restriction sites are added automatically by the programs, additional features are added manually to the map. 
