Efficient algorithms and software for detection of full-length LTR retrotransposons.

Proceedings. IEEE Computational Systems Bioinformatics Conference Pub Date : 2005-01-01 DOI:10.1109/csb.2005.31

Anantharaman Kalyanaraman, Srinivas Aluru

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引用次数: 8

Abstract

LTR retrotransposons constitute one of the most abundant classes of repetitive elements in eukaryotic genomes. In this paper, we present a new algorithm for detection of full-length LTR retrotransposons in genomic sequences. The algorithm identifies regions in a genomic sequence that show structural characteristics of LTR retrotransposons. Three key components distinguish our algorithm from that of current software - (i) a novel method that preprocesses the entire genomic sequence in linear time and produces high quality pairs of LTR candidates in running time that is constant per pair, (ii) a thorough alignment-based evaluation of candidate pairs to ensure high quality prediction, and (iii) a robust parameter set encompassing both structural constraints and quality controls providing users with a high degree of flexibility. Validation of both our serial and parallel implementations of the algorithm against the yeast genome indicates both superior quality and performance results when compared to existing software.

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全长LTR反转录转座子检测的有效算法和软件。

LTR逆转录转座子是真核生物基因组中最丰富的重复元件之一。本文提出了一种检测基因组序列中LTR逆转录转座子全长的新算法。该算法识别基因组序列中显示LTR反转录转座子结构特征的区域。我们的算法与当前的软件有三个关键的区别:(i)一种新颖的方法，在线性时间内预处理整个基因组序列，并在运行时间内产生每对恒定的高质量LTR候选对，(ii)对候选对进行全面的基于比对的评估，以确保高质量的预测，以及(iii)一个包含结构约束和质量控制的鲁棒参数集，为用户提供高度的灵活性。我们对酵母基因组算法的串行和并行实现验证表明，与现有软件相比，该算法的质量和性能都优于现有软件。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Proceedings. IEEE Computational Systems Bioinformatics Conference

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