nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms.
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.
Yao
Jiqiang
J
Citrus Research Board, 323 W. Oak, P.O. Box 230, Visalia, CA 93279, USA.
Lin
Hong
H
Doddapaneni
Harshavardhan
H
Civerolo
Edwin L
EL
D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment; D017385:Sequence Homology; D012984:Software; D014974:Xanthomonas / Q000145:classification / Q000235:genetics*