Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA

被引：82

作者：

Freyhult, Eva K.

Bollback, Jonathan P.

Gardner, Paul P. ^{[1
]}

机构：

[1] Univ Copenhagen, Inst Mol Biol & Physiol, Mol Evolut Grp, DK-2100 Copenhagen, Denmark

[2] Univ Copenhagen, Inst Biol, Evolut Dept, DK-2100 Copenhagen, Denmark

[3] Uppsala Univ, Linnaeus Ctr Bioinformat, S-75124 Uppsala, Sweden

来源：

GENOME RESEARCH | 2007年 / 17卷 / 01期

关键词：

D O I：

10.1101/gr.5890907

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：117 / 125

页数：9

共 56 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].