OGRe: a relational database for comparative analysis of mitochondrial genomes

Abstract

Organellar Genome Retrieval (OGRe) is a relational database of complete mitochondrial genome sequences for over 250 Metazoan species. OGRe provides a resource for the comparative analysis of mitochondrial genomes at several levels. At the sequence level, OGRe allows the retrieval of any selected set of mitochondrial genes from any selected set of species. Species are classified using a taxonomic system that allows easy selection of related groups of species. Sequence alignments are also available for some species. At the level of individual nucleotides, the system contains information on base frequencies and codon usage frequencies that can be compared between organisms. At the level of whole genomes, OGRe provides several ways of visualizing information on gene order. Diagrams illustrating the genome arrangement can be generated for any selected set of species automatically from the information in the database. Searches can be done based on gene arrangement to find sets of species that have the same order as one another. Diagrams for pairwise comparison of species can be produced that show the positions of break-points in the gene order and use colour to highlight the sections of the genome that have moved. OGRe is available from http://www.bioinf.man.ac.uk/ogre.

Figure 1

An example of three genome diagrams produced by the OGRe genome viewer.

Figure 2

An example of a pairwise genome comparison produced by OGRe where tRNA genes are included. The blocks of genes coloured red and yellow have exchanged positions between human and chicken but all genes remain on the same strand.

Figure 3

An example of a pairwise genome comparison produced by OGRe where tRNA genes are excluded. There are apparently three separate inversions of blocks of genes between human and locust (shown in red, yellow and blue). The grey and green gene blocks are unchanged.