Ellis, J. C. 2020. BMC Genomics

P Finder:  Genomic and metagenomic annotation of RNAse P RNA gene (rnpB)

J. Christopher Ellis
BMC Genomics 21: 334; doi: 10.1186/s12864-020-6615-z


The rnpB gene encodes for an essential catalytic RNA (RNase P). Like other essential RNAs, RNase P’s sequence is highly variable. However, unlike other essential RNAs (i.e. tRNA, 16 S, 6 S,…) its structure is also variable with at least 5 distinct structure types observed in prokaryotes. This structural variability makes it labor intensive and challenging to create and maintain covariance models for the detection of RNase P RNA in genomic and metagenomic sequences. The lack of a facile and rapid annotation algorithm has led to the rnpB gene being the most grossly under annotated essential gene in completed prokaryotic genomes with only a 24% annotation rate. Here we describe the coupling of the largest RNase P RNA database with the local alignment scoring algorithm to create the most sensitive and rapid prokaryote rnpB gene identification and annotation algorithm to date.


Ellis, J.C. P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB). BMC Genomics 21, 334 (2020). https://doi.org/10.1186/s12864-020-6615-z 

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