Affiliations: Citrus Research Board, 323 W. Oak, P.O. Box 230,
Visalia, CA 93279, USA | USDA-ARS, 9611 So. Riverbend Ave. Parlier, CA 93648,
USA | University of California, Davis, Department of
Viticulture and Enology, Davis, CA 95616, USA
Abstract: The increasing number of whole genomic sequences of microorganisms
has led to the complexity of genome-wide annotation and gene sequence
comparison among multiple microorganisms. To address this problem, we have
developed nWayComp software that compares DNA and protein sequences of
phylogenetically-related microorganisms. This package integrates a series of
bioinformatics tools such as BLAST, ClustalW, ALIGN, PHYLIP and PRIMER3 for
sequence comparison. It searches for homologous sequences among multiple
organisms and identifies genes that are unique to a particular organism. The
homologous gene sets are then ranked in the descending order of the sequence
similarity. For each set of homologous sequences, a table of sequence identity
among homologous genes along with sequence variations such as SNPs and INDELS
is developed, and a phylogenetic tree is constructed. In addition, a common set
of primers that can amplify all the homologous sequences are generated. The
nWayComp package provides users with a quick and convenient tool to compare
genomic sequences among multiple organisms at the whole-genome level.
Keywords: Sequence comparison, homology, unique, SNP, INDEL, Phylip, primer
