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Article type: Research Article
Authors: Yao, Jiqiang | Lin, Hong | Doddapaneni, Harshavardhan | Civerolo, Edwin L.
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
Note: [] Corresponding author. Tel.: +1 559 596 2702; E-mail: eciverolo@fresno.ars.usda.gov
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
Journal: In Silico Biology, vol. 7, no. 2, pp. 195-200, 2007
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