A central innovation in PlasMapper is its capacity to automatically identify and label the plasmid control sequences found in both eukaryotic and prokaryotic vectors using a large database of common plasmid sequences and common plasmid subsequences (replication origins, promoters, terminators, marker genes, etc.). Here we describe a web server, called PlasMapper, which is able to accept FASTA-formatted DNA sequences and generate a fully labeled/annotated plasmid map (both graphical and textual output) with essentially no further user input. One obvious solution is a plasmid mapping web server. Furthermore, with the increasing diversity of operating systems seen in many laboratories and the expanding level of inter-laboratory and international collaboration, we believe that a platform-independent solution to plasmid mapping is needed. With the growing trend toward using freeware and freely available web tools in bioinformatics, it seems that the continuing dependency on expensive commercial packages to perform just a single operation (plasmid mapping) is somewhat questionable. 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 Many of these early freeware packages have since been replaced by more sophisticated and far more user-friendly commercial packages such as SimVector (Premier BioSoft), GeneTool (BioTools), VectorNTI (Informax, Invitrogen),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. Received FebruRevised and Accepted MaINTRODUCTION 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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