'Gene neighbors' is a collection of databases and tools that can help identify gene neighbors based on user defined boundaries and overlaps. At least in prokaryotic genomes, these gene neighbors may represent operons, or operon-like gene arrangements.

Retrieving results from our database using the form displayed below is straightforward and easy. However, if you would like more help, or want more information, please write to: svdate AT ccwf dot cc dot utexas dot edu or marcotte AT icmb dot utexas dot edu.
Step 1: Select any completely sequenced genome of interest (you can choose individual chromosomes, plasmids or scaffolds, where available).




Step 2: Decide on maximum overlap allowed between gene boundries and maximum distance allowed between genes for them to be neighbors

Enter maximum distance allowed between two genes (default is 40 nucleotides, a -ve number will return overlapping genes)
Enter maximum overlap allowed between two genes (default is 50 nucleotides)


Step 3: Select any particular orientation of genes (say when one gene in on the plus strand and the neighbor is on the minus strand) that you want to exclude. Genes in the Plus/Minus and Minus/Plus orientations are excluded by default, however, you can choose to include them.

Exclude genes in Minus/Minus oreintation (<--, <--)
Exclude genes in Minus/Plus oreintation (<--, -->)
Exclude genes in Plus/Minus oreintation (-->, <--)
Exclude genes in Plus/Plus oreintation (-->, -->)


Step 4: Choose display of results.

Display all gene pairs
Display all genes neighbors


   
References

  • Date, S.V. & Marcotte, E. M. Protein function prediction using the Protein Link Explorer (PLEX) (manuscript in preparation, 2003).


  • Dandekar, T., Snel, B., Huynen, M. & Bork, P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324-328 (1998) [ PubMed ]


  • Salgado, H., Moreno-Hagelsieb, G., Smith, T. F. & Collado-Vides, J. Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci U S A. 97, 6652-6657 (2000) [ PubMed ]
    • Copyright © 2002, 2003, Shailesh Date and Edward Marcotte. The protein link explorer data and server is the property of the University of Texas, and cannot be used for commercial purposes without written permission of Edward Marcotte and the University of Texas. It is forbidden to redistribute, derivatize, or encapsulate the protein link explorer data or server in another database without permission. Sale of information derived from it, whether directly or in revised form, is forbidden except by permission of UT and Edward Marcotte. All copies or mirrors of the protein link explorer must carry this notice.