Bcheck: a wrapper tool for detecting RNase P RNA genes.

BMC Genomics
Dilmurat YusufIvo L Hofacker

Abstract

Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily specific descriptor models and covariance models. 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, Bcheck predictions have more intact structure and are automatically classified by subfamily membership. For eukaryotic chromosomes Bcheck could identify the known RNase P RNA genes in 84 out of 85 metazoan genomes and 19 out of 21 fungi genomes. Bcheck 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 ...Continue Reading

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Citations

Nov 11, 2010·Nucleic Acids Research·Paul P GardnerAlex Bateman
Dec 3, 2015·Environmental Microbiology·Salla T JaakkolaDennis H Bamford
Sep 6, 2015·Molecular Biology and Evolution·Marcus LechnerAnthony Gobert
Dec 6, 2011·Biochimica Et Biophysica Acta·Walter Rossmanith
Jan 15, 2015·Nucleic Acids Research·Jörg LindeOliver Kurzai
Nov 28, 2017·Genome Biology and Evolution·Wen-Sui Lo, Chih-Horng Kuo

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Software Mentioned

ushuffle
RNAmot
tRNAscan
fasta
blast
Bcheck
rnabob
RNAfold
MUSCLE
PatScan

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