Currently there are remarkably few freeware plasmid mapping programs still available, although pDRAW32 (AcaClone) is one example of an installable standalone package that supports plasmid mapping. Many of these early freeware packages have since been replaced by more sophisticated and far more user-friendly commercial packages such as SimVector (Premier BioSoft), GeneTool (BioTools), VectorNTI (Informax, Invitrogen), MacVector (Accelrys), DNA Strider and LaserGene (DNAStar). As early as the 1980s standalone computer programs were being described that supported the presentation and manipulation of plasmid maps on specific platforms and computer operating systems ( 1– 7). Because of the size and complexity of plasmid molecules, computer-generated maps are absolutely essential to identify, locate and analyze key regions in a vector sequence. Indeed, probably almost every practicing molecular biologist has worked with or generated a plasmid map to guide them through the cloning or plasmid manipulation process. Plasmid map generation is one of the oldest and most frequently performed operations in bioinformatics. The PlasMapper web server is freely accessible at. The images and textual output are of sufficient quality that they may be used directly in publications or presentations. Further, PlasMapper images can be rendered in both rasterized (PNG and JPG) and vector graphics (SVG) formats to accommodate a variety of user needs or preferences. The appearance and contents of the output can be customized in numerous ways using several supplied options. PlasMapper then presents the identified features in textual form and as high-resolution, multicolored graphical output. Taking only the plasmid/vector DNA sequence as input, PlasMapper uses sequence pattern matching and BLAST alignment to automatically identify and label common promoters, terminators, cloning sites, restriction sites, reporter genes, affinity tags, selectable marker genes, replication origins and open reading frames. PlasMapper is a comprehensive web server that automatically generates and annotates high-quality circular plasmid maps.
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