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In Silico Biology 7, 0020 (2007); ©2007, Bioinformation Systems e.V.  

nWayComp: A genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms

Jiqiang Yao1, Hong Lin2, Harshavardhan Doddapaneni3, and Edwin L. Civerolo2*

1 Citrus Research Board, 323 W. Oak, P.O. Box 230, Visalia, CA 93279, USA
2 USDA-ARS, 9611 So. Riverbend Ave. Parlier, CA 93648, USA
3 University of California, Davis, Department of Viticulture and Enology, Davis, CA 95616, USA

* Corresponding author

Edited by E. Wingender; received December 18, 2006; revised February 20, 2007; accepted February 24, 2007; published February 28, 2007


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 ascending 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