Nucleic Acids Research Advance Access published online on May 8, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp327
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Orphelia: predicting genes in metagenomic sequencing reads
1Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany and 2Center for Genomic Regulation, Comparative Bioinformatics Research Group, Biomedical Research Park, c/Dr. Aiguader 88, 08003 Barcelona, Spain
*To whom correspondence should be addressed: Tel: +49 551 391 3884; Fax +49 551 391 4929; Email: katharina{at}gobics.de
Received February 13, 2009. Revised April 20, 2009. Accepted April 20, 2009.
Metagenomic sequencing projects yield numerous sequencing reads of a diverse range of uncultivated and mostly yet unknown microorganisms. In many cases, these sequencing reads cannot be assembled into longer contigs. Thus, gene prediction tools that were originally developed for whole-genome analysis are not suitable for processing metagenomes. Orphelia is a program for predicting genes in short DNA sequences that is available through a web server application (http://orphelia.gobics.de). Orphelia utilizes prediction models that were created with machine learning techniques on the basis of a wide range of annotated genomes. In contrast to other methods for metagenomic gene prediction, Orphelia has fragment length-specific prediction models for the two most popular sequencing techniques in metagenomics, chain termination sequencing and pyrosequencing. These models ensure highly specific gene predictions.