Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA
Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA
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DOI：
10.1101/gr.5890907
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发表时间：
2007-01-01
期刊：
影响因子：
7
通讯作者：
Gardner, Paul P.
中科院分区：
文献类型：
--
作者：
Freyhult, Eva K.;Bollback, Jonathan P.;Gardner, Paul P.
同源性搜索是最普遍的生物信息学任务之一，然而目前可用的工具用于识别非编码RNA（ncRNA）的有效性尚不清楚。在这项工作中，我们使用可靠的ncRNA数据集来评估BLAST，FASTA，HMMer和Infernal等方法的有效性。令人惊讶的是，最流行的同源性搜索方法往往是最不准确的。因此，许多研究使用了不适当的分析工具。在我们的研究结果的基础上，我们提出了同源性搜索策略，使用目前可用的工具和未来发展的一些方向。
Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness of methods such as BLAST, FASTA, HMMer, and Infernal. Surprisingly, the most popular homology search methods are often the least accurate. As a result, many studies have used inappropriate tools for their analyses. On the basis of our results, we suggest homology search strategies using the currently available tools and some directions for future development.