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

TitlenWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms.
Publication TypeJournal Article
Year of Publication2007
AuthorsYao, J, Lin, H, Doddapaneni, HV, Civerolo, EL
JournalIn Silico Biol
Volume7
Issue2
Pagination195-200
Date Published2007
ISSN1386-6338
KeywordsComputational Biology, Databases, Genetic, Genes, Bacterial, Genome, Bacterial, Multigene Family, Phylogeny, Sequence Alignment, Sequence Homology, Software, Xanthomonas
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.

Alternate JournalIn Silico Biol. (Gedrukt)
PubMed ID17688445