|Title||nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms.|
|Publication Type||Journal Article|
|Year of Publication||2007|
|Authors||Yao, J, Lin, H, Doddapaneni, H, Civerolo, EL|
|Journal||In Silico Biol|
|Keywords||Computational Biology, Databases, Genetic, Genes, Bacterial, Genome, Bacterial, Multigene Family, Phylogeny, Sequence Alignment, Sequence Homology, Software, Xanthomonas|
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.
|Alternate Journal||In Silico Biol|