Retrogenomic software and databases to solve evolutionary questions

近二十年来，逆转录因子活动的痕迹被用于研究脊椎动物不同分支之间和内部的系统发育关系。在哺乳动物中，利用反转录子的插入作为系统发育标记已经解决了许多系统发育问题。然而，世界上只有少数实验室成功有效地应用了逆转录因子来研究进化。最有问题的任务是筛选基因组数据，从数十万插入保守基因组位点的反转录子中选择少数能够提供可靠系统发育结果的反转录子。深入了解不同逆转录因子的性质和高通量的生物信息学支持对这些研究至关重要；然而，很少有生物信息学工具可用于支持这一领域的研究。在过去的十年中，我们小组收集了大量的经验，并制定了许多使用逆转录因子作为系统发育标记的策略。我们开发了几种计算性的高通量策略，并将其应用于后系统基因组重建。我们现在已经开始将我们的知识转化为有用的、基于网络的生物信息学应用。TinT和GPAC工具，由科学家要求选择提取反转录子元件作为潜在的系统发育信息标记，已经在网上可用，但需要一个更彻底的，综合的方法。我们打算建立一个模块化的生物信息学框架，用于规划基于反转录子标记的反转录系统基因组项目，并分析在实验和计算机研究中获得的反转录元件的存在/缺失模式。我们计划将这些工具免费提供给科学界，并将它们整合到全球活跃的基因组测序项目框架中。新的工具和数据库将保存在本地计算机服务器上，并不断发展和更新。

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.