The PATIMDB Application

The PATIMDB application is a tool designed to assist in the generation of bacterial transposon insertion mutant libraries, such as the PA14 Transposon Insertion Mutant Library. It is assumed that users of the application will generate their mutant library by the method of Liberati et al.

The application provides two main types of functionality:

  1. Process tracking
  2. Automated Sequence Analysis

Researchers using protocols similar to that of Liberati et al. will find the PATIMDB application most useful because the application in its current form makes some assumptions about experimental setup, and how plates are copied and replicated. But even if users employ a different procedure, to generate and sequence their transposon insertion mutant library, the Automated Sequence Analysis functions of the PATIMDB application will still be useful. A detailed description of the installation and use of the PATIMDB Application is has been published in Current Protocols in Molecular Biology (Urbach et. al).

The PATIMDB Application is available for download here. Note, there are two packages available, one with a .zip suffix, and one with a .tgz suffix. They have the same contents, and are provided for convenience, since .zip is preferred on Windows, and .tgz is most convenient on UNIX and Unix-like operating systems, such as Mac OS X and Linux.

Downloads

PATIMDB_app_20091111.zip
PATIMDB_app_20091111.tgz

Documentation

The PATIMDB Application Documentation is available here.

References

  1. Liberati NT, Urbach JM, Miyata S, Lee DG, Drenkard E, Wu G, Villanueva J, Wei T, Ausubel FM. (2006) An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc Natl Acad Sci U S A. 103:2833-8.
  2. Urbach JM, Wei T, Liberati N, Grenfell-Lee D, Villanueva J, Wu G, Ausubel FM. (2009) Using PATIMDB to create bacterial transposon insertion mutant libraries. Curr Protoc Mol Biol. 2009 Apr;Chapter 19:Unit 19.7.

Contact:
Jonathan M. Urbach
Email: urbach@molbio.mgh.harvard.edu
Revised: