2021
DOI: 10.1186/s13059-021-02319-w
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Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

Abstract: Background Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations. Results … Show more

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Cited by 6 publications
(5 citation statements)
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“…There are several limitations to our comparative genomics approach, consistent with similar approaches performed previously [1][2][3]. First, this method does not validate RNA structures experimentally using methods like SHAPE-Seq or FragSeq for the majority of predictions [51,52].…”
Section: Discussionmentioning
confidence: 92%
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“…There are several limitations to our comparative genomics approach, consistent with similar approaches performed previously [1][2][3]. First, this method does not validate RNA structures experimentally using methods like SHAPE-Seq or FragSeq for the majority of predictions [51,52].…”
Section: Discussionmentioning
confidence: 92%
“…We also removed duplicate csRNAs that matched any of the same regions as another csRNA by choosing the longest structure, resulting in 8890 csRNAs. Among these, 324 were already present in Rfam [36] and 71 were recently identified in human microbiomes [2], resulting in a finalized set of 8495 novel csRNAs (Fig. 1A).…”
Section: Workflows To Predict Csrnasmentioning
confidence: 99%
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