Welcome to the OG1RF Transposon Insertion Mutant Database
Danielle A. Garsin, Jonathan M. Urbach and Frederick M. Ausubel
In order to define the pathogenic processes involved in Enterococcus faecalis
infection, an Ordered Library has been produced. The Library consists
of a collection of non-redundant transposon insertions in approximately
25% of the non-essential open reading frame in the genome of Enterococcus faecalis
strain OG1RF. This strain has been shown to cause disease in a variety
of hosts. We are currently considering both technical and funding
mechanisms to complete the library.
the construction of the OG1RF Ordered Library, approximately 8,865
transposon insertions were sequenced. To track and sort these mutants,
an OG1RF Transposon Insertion Mutant Database has been developed.
Sequence data from the stretch of DNA adjacent to the transposon were
entered into the database and aligned with sequences from the E. faecalis strain V583 genome (http://www.tigr.org/tigr-scripts/CMR2/GenomePage3.spl?database=gef)
using the BLAST algorithm. The database identifies the V583 ORF and the
location within that ORF that corresponds to the site that is disrupted
by each transposon insertion in the related OG1RF strain. Therefore,
the reported transposon insertion site for each mutant corresponds to a
"virtual" location in the V583 genome that corresponds to a known
location in the OG1RF genome.
Mutants that have a transposon
insertion site within a region corresponding to a predicted V583 ORF
are available for searches. In many cases we have more than one mutant
representing a particular ORF.
The database lists 4 fields that may be queried for each mutant:
Mutant ID: The unique identifier for each mutant in the database
Plate Location: The physical location of the mutant in a microtiter plate within our storage system
If you use any mutants to generate data for publication, please
acknowledge "Massachusetts General Hospital and Harvard Medical School,
Boston, MA(http://ausubellab.mgh.harvard.edu/enterococcus) [date,(month
and yr) accessed]"
The Library and Database
are still in development. Please bring any problems you may encounter
to our attention. For problems related to the mutants, contact Danielle.A.Garsin@uth.tmc.edu. For issues regarding the database contact email@example.com. General feedback is also welcome.
This work was supported by grants from Aventis, SA and NHLBI grant UO1 HL66678 to F.M.A. and NSF grant MCB-0315316 to J.E.P.
The Enterococcus faecalis database, workflow, and
methodology were created using technology developed by Nicole Liberati,
Jas Villanueva, Dan Lee, Tao Wei, Gang Wu, Jonathan Urbach, and Fred