POSTER ABSTRACTS 63
“A Computational Process To Locate IS Elements And Study Horizontal Gene Transfer In Bacterial Genomes” Walter J. Lewis*2, Wenyi Bi2, Sean R. McCorkle 1, Daniel Van DerLie1 1Brookhaven National Laboratory, Upton, NY 2Cheyney University of Pennsylvania, Cheyney, PA Abstract Currently there is a tremendous focus on studying how whole units of DNA are shared between species. These movable tracks of DNA, called transposons, are demarcated by shorter insertion sequence (IS) elements, which themselves are generally around 700 to 2500 bp in length, and code for proteins implicated in transposition activity, such as transposase and intergrase. IS elements are bracketed by pairs of inverted repeats of variant length (approx. 10 ‐30 bp), and are further embedded in a pair of short direct repeats of approximately 3 – 7 bp. While there is a great deal of software to automatically annotate genes and regulatory regions, there are currently no programs to identify IS elements de novo. Hundreds of completed bacterial genomes are currently available and more are constantly being added to that list, which makes it increasingly important for the computational detection of IS elements. To this end, we have developed a C++ program to locate IS elements in bacterial genomes. The process was broken down into steps in order to make it more dynamic so that one could easily examine the data in each stage of the process to detect errors, or perhaps discover something unexpected. First, all repeats (within length constraints) are reported, and then these are searched for pairs of inverted repeats which have the proper orientation and distance. Positions, paired inverted repeat sequences, and interior coding sequences are reported for these IS element candidates. Lastly the interior coding sequences are examined for homology with known transposition genes. Preliminary tests on the genome of Enterobacter strain 638, recently sequenced as part of the DOE biofuels initiative, revealed 9 putative IS candidates, 6 of which were confirmed by Blastx searches of Genbank, which yielded strong homology matches to transposase and intergrase in other organisms. Further testing on an IS‐rich genome, now Cupriavidus metallidurans (CH34), will allow us to optimize program parameters to improve performance. Because this process reports direct and inverted sequence pairs, which travel along with the IS element as it moves, it can be used to trace horizontal gene transfer history within or between genomes for evolutionary studies. 217