MICROBIAL & COMPARITIVE GENOMICS
Volume 2, Number 2, 1997
MAry Ann Liebert, Inc.
GRS: A Graphic Tool for Genome Retrieval and Segment Analysis
Thomas Sicheritz-Pontén and Siv G.E. Andersson
ABSTRACT
GRS is a graphic tool for retrieval and visualization of genome
segments from partially or completely sequenced genomes. To facilitate
visual identification of conserved genomic motifs, genes are
color-coded according to their presumed functional roles. Aligned
genes can be rapidly screened for potential homology by automatic
retrieval and alignment of the corresponding protein
sequences. Furthermore, the map location of any genome segment can be
visually compared to the position of the same segment in other genomes
or to the position of other segments within the same genome. The gene
string analysis option of GRS allows the identification of genes that
are identically arranged in any pairwise set of genomes. Finally, the
program allows the user to create new gene table format file to enable
comparisons of gene order structures in recently determined sequence
data to the patterns of genes in already existing microbial and
organellar databases. With the help of GRS, the genomic contexts of
genes for which no identifiable homologues exist can be analyzed to
provide an additional source of information for sequence
annotations. We illustrate the use of GRS by analyzing the structure
and distribution of phylogenetically conserved motifs in closely as
well as more distantly related microbial genomes.