RNAmmer: consistent and rapid annotation of ribosomal RNA genes

Autor:	David W. Ussery, Torbjørn Rognes, Karin Lagesen, Hans Henrik Stærfeldt, Peter Fischer Hallin, Einar Andreas Rødland
Jazyk:	angličtina
Rok vydání:	2007
Předmět:	Genetics Gene prediction 5.8S ribosomal RNA Intron Computational Biology Genes rRNA Computational biology Genomics Ribosomal RNA Biology 18S ribosomal RNA Markov Chains 5S ribosomal RNA 28S ribosomal RNA Minimal genome Genome Bacterial Software
Zdroj:	Nucleic Acids Research
ISSN:	1362-4962 0305-1048
Popis:	The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA genes difficult. We have therefore created computational predictors for the major rRNA species from all kingdoms of life and compiled them into a program called RNAmmer. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. A pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy. Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e9f0c7161656b4f141b727d7020c9193 http://europepmc.org/articles/PMC1888812 Zobrazit plný text záznamu