Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada.
BMC Bioinformatics. 2013 Jun 7;14:186. doi: 10.1186/1471-2105-14-186.
Miniature inverted repeat transposable elements (MITEs) are abundant non-autonomous elements, playing important roles in shaping gene and genome evolution. Their characteristic structural features are suitable for automated identification by computational approaches, however, de novo MITE discovery at genomic levels is still resource expensive. Efficient and accurate computational tools are desirable. Existing algorithms process every member of a MITE family, therefore a major portion of the computing task is redundant.
In this study, redundant computing steps were analyzed and a novel algorithm emphasizing on the reduction of such redundant computing was implemented in MITE Digger. It completed processing the whole rice genome sequence database in ~15 hours and produced 332 MITE candidates with low false positive (1.8%) and false negative (0.9%) rates. MITE Digger was also tested for genome wide MITE discovery with four other genomes.
MITE Digger is efficient and accurate for genome wide retrieval of MITEs. Its user friendly interface further facilitates genome wide analyses of MITEs on a routine basis. The MITE Digger program is available at: http://labs.csb.utoronto.ca/yang/MITEDigger.
微型反向重复转座元件（MITEs）是丰富的非自主元件，在塑造基因和基因组进化方面发挥着重要作用。它们的特征结构特征适合通过计算方法进行自动识别，然而，在基因组水平上进行新的 MITE 发现仍然需要大量资源。高效、准确的计算工具是理想的。现有的算法处理 MITE 家族的每一个成员，因此计算任务的很大一部分是冗余的。
在这项研究中，分析了冗余的计算步骤，并在 MITE Digger 中实现了一种强调减少这种冗余计算的新算法。它在大约 15 小时内完成了整个水稻基因组序列数据库的处理，并产生了 332 个 MITE 候选物，假阳性率（1.8%）和假阴性率（0.9%）都很低。MITE Digger 还被用于对另外四个基因组进行全基因组 MITE 发现测试。
MITE Digger 是一种高效、准确的全基因组 MITE 检索工具。其用户友好的界面进一步促进了 MITE 全基因组分析的常规进行。MITE Digger 程序可在以下网址获得：http://labs.csb.utoronto.ca/yang/MITEDigger。
