Is reciprocal best hit method applicable for non-coding RNA to find orthologs?
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9 months ago
jirathnuan • 0

Hello,

I'm trying to identify orthologous non-coding RNAs among multiple species. And information of ncRNAs are not well annotated in the genome. So that I choose BLAST in attempt to find orthologous ncRNA between them.

One of the methods to infer the orthologous sequences I've found is to infer from their reciprocal best hits, but usually applied to the protein-coding genes (like in this article: https://doi.org/10.1186/s12864-020-07132-6)

Could this approach also be applied to ncRNAs? Any other suggestions or approaches would be appreciated.

Thanks

ncRNA BLAST ortholog • 665 views
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Entering edit mode
9 months ago
DareDevil ★ 4.3k

The reciprocal best hit (RBH) method is primarily used to identify orthologous genes in coding sequences or protein sequences. It relies on the assumption that orthologous genes, which have evolved from a common ancestral gene, are likely to be each other's best match in different species.

For non-coding RNA (ncRNA), the RBH method may not be as applicable or reliable. This is because ncRNAs, such as microRNAs, transfer RNAs, and ribosomal RNAs, have distinct secondary structures and functional regions, which may result in more diverse sequence conservation patterns compared to protein-coding genes. In addition, ncRNAs often evolve through mechanisms like duplication, transposition, and rapid sequence divergence, which can further complicate the identification of orthologs using sequence similarity alone.

Nevertheless, some studies have adapted or modified the RBH method for identifying orthologous ncRNAs. These adaptations may involve considering additional structural and functional features of ncRNAs beyond sequence similarity alone. Other approaches, such as phylogenetic analysis or conservation of secondary structures, can also be employed to infer orthology among ncRNAs.

RBH method is primarily used for coding sequences or proteins, it may be modified or combined with other approaches to identify orthologous ncRNAs. However, the unique characteristics of ncRNAs require additional considerations beyond sequence similarity for accurate orthology inference.

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9 months ago

Yes, the reciprocal best BLAST hit method is suitable for identifying orthologous non-coding RNAs. When two non-coding RNAs from different species are identified as the top hits in both forward and reverse BLASTn searches, considering the context of their entire genomes, it strongly suggests that they are orthologous.

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