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PlasMapper: a web server for drawing and auto-annotating plasmid maps.

Xiaoli Dong1, Paul Stothard, Ian J Forsythe

  • 1Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada.

Nucleic Acids Research
|June 25, 2004
PubMed
Summary
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PlasMapper is a web server that automatically generates annotated circular plasmid maps from DNA sequences. This tool aids researchers by identifying key genetic elements for publication-quality figures.

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Plasmid maps are essential for visualizing genetic elements in molecular biology.
  • Manual generation of plasmid maps is time-consuming and prone to errors.
  • Automated tools are needed to streamline plasmid annotation and visualization.

Purpose of the Study:

  • To develop a comprehensive web server for automatic generation and annotation of circular plasmid maps.
  • To provide researchers with high-quality, customizable plasmid visualizations for publications and presentations.

Main Methods:

  • PlasMapper accepts plasmid/vector DNA sequences as input.
  • It utilizes sequence pattern matching and BLAST alignment to identify genetic features.
  • Features identified include promoters, terminators, cloning sites, restriction sites, reporter genes, affinity tags, selectable marker genes, replication origins, and open reading frames.

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Main Results:

  • PlasMapper automatically generates annotated circular plasmid maps with high-quality graphical and textual output.
  • The tool identifies and labels a wide range of common genetic elements.
  • Output is customizable and available in rasterized (PNG, JPG) and vector (SVG) formats.

Conclusions:

  • PlasMapper provides an efficient and accurate solution for plasmid map generation and annotation.
  • The generated maps are suitable for direct use in scientific publications and presentations.
  • The web server is freely accessible, supporting molecular biology research.