TBI-p-2010-2
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Titel:
Bcheck: a wrapper tool for detecting RNase P RNA genes
Author(s):
Dilmurat Yusuf, Manja Marz, Peter F. Stadler, Ivo L. Hofacker
submitted to:
Abstract:
Background: Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome
annotation. We present Bcheck, a wrapper tool for predicting 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.
Results: Scanning all microbial genomes in GenBank identifies the RNase P RNA 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 gene in 84 out of
85 metazoan genomes, 19 out of 21 fungi genomes. Bcheck predicted 37 novel eukaryotic RNase P RNAs, 32
of which are from fungi organisms. 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 falls into ancestral bacteria A type of RNase
P RNA and 66% of which have no close homolog to known prokaryotic RNase P RNAs.
Conclusions: The combination of efficient filtering by means of a descriptor-based search and subsequent con-
struction of a high-quality gene model by means of a covariance model provides an efficient method for the
detection of RNase P RNAs in large-scale sequencing data.
Bcheck is implemented as webserver and can also be downloaded for local use from http://rna.tbi.univie.ac.at/
bcheck/index.html
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Last modified: 2008-10-22 12:23:11 fall