REGANOR: A gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes

Abstract

With >1000 prokaryotic genome sequencing projects ongoing or already finished, comprehensive comparative analysis of the gene content of these genomes has become viable. To allow for a meaningful comparative analysis, gene prediction of the various genomes should be as accurate as possible. It is clear that improving the state of genome annotation requires automated gene identification methods to cope with the influence of artifacts, such as genomic GC content. There is currently still room for improvement in the state of annotations. We present a web server and a database of high-quality gene predictions. The web server is a resource for gene identification in prokaryote genome sequences. It implements our previously described, accurate gene finding method REGANOR. We also provide novel gene predictions for 241 complete, or almost complete, prokaryotic genomes. We demonstrate how this resource can easily be utilised to identify promising candidates for currently missing genes from genome annotations with several examples. All data sets are available online. Availability: The gene finding server is accessible via https://www.cebitec.uni-bielefeld.de/groups/brf/software/reganor/cgi-bin/ reganor_upload.cgi. The server software is available with the GenDB genome annotation system (version 2.2.1 onwards) under the GNU general public license. The software can be downloaded from https://sourceforge.net/projects/gendb/. More information on installing GenDB and REGANOR and the system requirements can be found on the GenDB project page http://www.cebitec.uni-bielefeld.de/groups/ brf/software/wiki/GenDBWiki/AdministratorDocumentation/GenDBInstallation. © 2006 Adis Data Information BV. All rights reserved.