UNIT 19.7 Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries

  1. Jonathan M. Urbach1,
  2. Tao Wei2,
  3. Nicole Liberati1,
  4. Daniel Grenfell-Lee3,
  5. Jacinto Villanueva4,
  6. Gang Wu1,
  7. Frederick M. Ausubel1

Published Online: 1 APR 2009

DOI: 10.1002/0471142727.mb1907s86

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Urbach, J. M., Wei, T., Liberati, N., Grenfell-Lee, D., Villanueva, J., Wu, G. and Ausubel, F. M. 2009. Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries. Current Protocols in Molecular Biology. 86:19.7:19.7.1–19.7.34.

Author Information

  1. 1

    Massachusetts General Hospital, Boston, Massachusetts

  2. 2

    Eli Lilly and Company, Indianapolis, Indiana

  3. 3

    Microbia Precision Engineering, Lexington, Massachusetts

  4. 4

    Mariposa Bioscience Inc., Burlingame, California

Publication History

  1. Published Online: 1 APR 2009
  2. Published Print: APR 2009


PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software. Curr. Protoc. Mol. Biol. 86:19.7.1-19.7.34. © 2009 by John Wiley & Sons, Inc.


  • transposon;
  • mutant;
  • library;
  • software;
  • process tracking;
  • pipeline