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Nucleic Acids Research Advance Access published online on August 7, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm597
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

A survey of bacterial insertion sequences using IScan

Andreas Wagner1,*, Christopher Lewis2 and Manuel Bichsel1

1Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 27-J-54, CH-8057 Zurich, Switzerland and 2Department of Biology, MSC03 2020,1 University of New Mexico, Albuquerque, NM, 87131-0001

*To whom correspondence should be addressed. Tel: +41 446356141; Fax: +41 44635 6144; Email: aw{at}bioc.uzh.ch

Received May 25, 2007. Revised July 19, 2007. Accepted July 19, 2007.

Bacterial insertion sequences (ISs) are the simplest kinds of bacterial mobile DNA. Evolutionary studies need consistent IS annotation across many different genomes. We have developed an open-source software package, IScan, to identify bacterial ISs and their sequence elements—inverted and target direct repeats—in multiple genomes using multiple flexible search parameters. We applied IScan to 438 completely sequenced bacterial genomes and 20 IS families. The resulting data show that ISs within a genome are extremely similar, with a mean synonymous divergence of Ks = 0.033. Our analysis substantially extends previously available information, and suggests that most ISs have entered bacterial genomes recently. By implication, their population persistence may depend on horizontal transfer. We also used IScan's ability to analyze the statistical significance of sequence similarity among many IS inverted repeats. Although the inverted repeats of insertion sequences are evolutionarily highly flexible parts of ISs, we show that this ability can be used to enrich a dataset for ISs that are likely to be functional. Applied to the thousands of genomes that will soon be available, IScan could be used for many purposes, such as mapping the evolutionary history and horizontal transfer patterns of different ISs.


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