Retrogenomic software and databases to solve evolutionary questions

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For nearly two decades, traces of the activities of retroposed elements have been used for examining the phylogenetic relationships among and within different clades of vertebrates. In mammals, many phylogenetic questions have already been resolved using insertions of retroposons as phylogenetic markers. However, only a few laboratories in the world have successfully and efficiently applied retroelements to investigate evolution. The most problematic task is screening genomic data to select from hundreds of thousands of retroposons inserted in conserved genomic loci the few that can provide reliable phylogenetic results. Profound knowledge of the nature of different retroelements and high-throughput bioinformatic support are essential for these studies; however, very few bioinformatics tools are available to support this area of research. During the last decade, our group collected a great deal of experience and developed many strategies for using retroelements as phylogenetic markers. We developed several computational, highthroughput strategies and applied those to retrophylogenomic reconstructions. We have now started to convert our knowledge into useful, web-based bioinformatic applications. The TinT and GPAC tools, requested by scientists for selecting extracting retroposon elements as potential phylogenetically informative markers, are already available on-line, but a more thorough, integrated approach is needed. We intend to derive a modular, bioinformatic framework for planning retrophylogenomic projects based on retroposon markers and for analyzing the presence/absence patterns of retroelements obtained in experimental and in silico research. We plan to make these tools freely available for the scientific community and to integrate them into the frameworks of world-wide active genomesequencing projects. The new tools and databases will be maintained on local computer servers and continuously developed and up-dated.