Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA
Freyhult E, Bollback JP, Gardner P. 2007. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. 17(1), 117–25.
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Journal Article
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Author
Freyhult, Eva K;
Bollback, Jonathan PISTA 
;
Gardner, Paul P
;
Gardner, Paul PAbstract
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.
Publishing Year
Date Published
2007-01-01
Journal Title
Genome Research
Volume
17
Issue
1
Page
117 - 25
IST-REx-ID
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Freyhult E, Bollback JP, Gardner P. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. 2007;17(1):117-125. doi:10.1101/gr.5890907
Freyhult, E., Bollback, J. P., & Gardner, P. (2007). Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.5890907
Freyhult, Eva, Jonathan P Bollback, and Paul Gardner. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” Genome Research. Cold Spring Harbor Laboratory Press, 2007. https://doi.org/10.1101/gr.5890907.
E. Freyhult, J. P. Bollback, and P. Gardner, “Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA,” Genome Research, vol. 17, no. 1. Cold Spring Harbor Laboratory Press, pp. 117–25, 2007.
Freyhult E, Bollback JP, Gardner P. 2007. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. 17(1), 117–25.
Freyhult, Eva, et al. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” Genome Research, vol. 17, no. 1, Cold Spring Harbor Laboratory Press, 2007, pp. 117–25, doi:10.1101/gr.5890907.
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