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

Eva Freyhult | Zendy; Jonathan P. Bollback | Zendy; Paul P. Gardner | Zendy

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

Author(s) -

Eva Freyhult,

Jonathan P. Bollback,

Paul P. Gardner

Publication year - 2006

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.5890907

Subject(s) - biology , computational biology , homology (biology) , non coding rna , rna , genomics , bioinformatics , genetics , gene , genome

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.

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