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United States Department of Agriculture

Agricultural Research Service

Title: nWayComp: A Tool for Universal Comparison of DNA and Protein Sequences

Authors
item Yao, Jiqiang - CITRUS RESEARCH BOARD
item Lin, Hong
item Doddapaneni, Harshavardhan - UNIV. OF CA, DAVIS
item Civerolo, Edwin

Submitted to: In Silico Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 24, 2007
Publication Date: February 28, 2007
Citation: Yao, J., Lin, H., Doddapaneni, H., Civerolo, E.L. 2007. nWayComp: A Tool for Universal Comparison of DNA and Protein Sequences. In Silico Biology. 7(2):195-200

Interpretive Summary: The rapidly increasing number of complete sequences available for microbes has facilitated comparison of microbial genomes at a level of detail not previously possible. Yet the shear volume of sequence data available has complicated whole genome comparisons among multiple organisms. To address this problem, we developed software called nWayComp which is able to compare DNA and protein sequence among multiple organisms. This software integrates a number of common computational tools for sequence analyses including Blast, ClustalW, ALIGN, PHYLIP and PRIMER3. The software produces a user-friendly output file in html format, which is linked to a mini-database containing homologous/unique gene sequences and alignments. This package provides users a quick and convenient tool for whole-genome sequence analysis. Using this package, we compared gene sequences of six strains of Xanthomonas spp. Common and unique genes of this group of organisms were readily identified, validating the utility of the software.

Technical Abstract: The increasing number of whole genomic sequences of microorganisms has increased the complexity of genome-wide annotation and gene sequence comparison among multiple microorganisms. To address this problem, we 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. The software 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 is generated and a phylogenetic tree is constructed. Sequence variations, such as SNPs and INDELS, are also identified for each homologous gene set. The software identifies a common set of primer pairs able to amplify all homologous sequences of a set. nWayComp was tested using whole genome sequence of six Xanthomonas strains. The resulting analysis validated the nWayComp package as a quick and convenient tool to compare genomic sequences among multiple organisms at the whole-genome level.

Last Modified: 12/18/2014
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