Bcheck: a wrapper tool for detecting RNase P RNA genes

Abstract

Abstract Background Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present , a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of is a library of subfamily specific descriptor models and covariance models. Results Scanning all microbial genomes in GenBank identifies RNase P RNA genes in 98% of 1024 microbial chromosomal sequences within just 4 hours on single CPU. Comparing to existing annotations found in 387 of the GenBank files, predictions have more intact structure and are automatically classified by subfamily membership. For eukaryotic chromosomes could identify the known RNase P RNA genes in 84 out of 85 metazoan genomes and 19 out of 21 fungi genomes. predicted 37 novel eukaryotic RNase P RNA genes, 32 of which are from fungi. Gene duplication events are observed in at least 20 metazoan organisms. Scanning of meta-genomic data from the Global Ocean Sampling Expedition, comprising over 10 million sample sequences (18 Gigabases), predicted 2909 unique genes, 98% of which fall into ancestral bacteria A type of RNase P RNA and 66% of which have no close homolog to known prokaryotic RNase P RNA. Conclusions The combination of efficient filtering by means of a descriptor-based search and subsequent construction of a high-quality gene model by means of a covariance model provides an efficient method for the detection of RNase P RNA genes in large-scale sequencing data. is implemented as webserver and can also be downloaded for local use from http://rna.tbi.univie.ac.at/bcheck