K. Byron, M.C.-Cervantes, J.T.L. Wang, W.C. Lin, and Y. Park

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Non-coding RNA, covariance model, secondary structure, Drosophila,comparative genomics


Evolutionarily conserved functional domains of non-coding RNA on chromosome X (roX1 ) have been identified in eight Drosophila species in a prior study. Among our findings, three GUUNUACG repeats were localized in the 3 -end of the predicted roX1 RNAs for these Drosophila species. In this study, we use a covariance model (CM) to search for the characteristic features of roX1 functional domains as a way to predict new examples of these structured RNAs in other Drosophila species, as sequencing data become available. We scan whole genomes of Drosophila and identify search results in available “region terms, i.e., “chromosome or “scaffold , depending on the annotation status of the particular species being surveyed. With known roX1 examples produced through our prior studies for support in comparative analysis, we hypothesize that it is possible to predict novel roX1 functional domains accurately from sequence information alone. Annotating roX1 on a genomic scale provides insight into evolutionary processes and phylogenetic relationships among the analyzed species. Based on our results, we confirmed that a CM search is effective in mining roX1 RNA genes and, that due to its inherent flexibility, this mining approach will likely prove successful for similar endeavours in various other organisms.

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