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Plasmi::db is a project management tool for molecular biology

Its database and associated tools allow:
  • Storage of sequence data
  • Automation of repetitive tasks, such as translation of open reading frames into protein sequences and molecular weight calculation
  • Cross-checking of nucleotide sequences and their properties, such as molecular weights and extinction coefficients of derived protein sequences
  • Sample labeling and tracking for downstream applications such as crystallogenesis
  • Oligonucleotide 'primer' design tools based on standard cloning strategies.
Since plasmid DNA is the tool of choice to produce protein, DNA or RNA products, by recombinant expression, restriction digestion or transcription, respectively, it is essential that the properties of plasmids are stored coherently.

Therefore, we have produced a tool which stores plasmid DNA sequences, their desired product sequences and helps keep a clear overview of the processes involved in vector construction.

Sample Image

Figure 1.

A user can attribute a protein "Target", to a Complex. This later allows the selection of targets according to the complex to which the target belongs. The "complex" page allows a quick overview of the various projects.

Sample Image

Figure 2.

When a complex is selected, the protein targets are sorted to that the complex subunits of interest are displayed.

This allows coherent storage of information about:

  • Standard cloning or expression plasmids (e.g. their antibiotic selection markers, any RNA polymerase promoters).
  • Database sequences you may be currently working on (their accession numbers, sequences, coding sequences).
  • Products you may wish to express or purify from them.  e.g. His-tagged protein or RNA run-off transcripts etc.
  • Primers you have ordered.
  • Restriction enzymes.
  • DNA sequencing data.
  • Protein prep yields and data about purity.
The database contains user and session information, so only upon logging-in, can one view and edit the database information.

Have a look at the screenshots to get an idea of what it can do.