The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes thr

Background: Data mining in large DNA sequences is a major challenge in microbial genomics and bioinformatics. Oligonucleotide usage (OU) patterns provide a wealth of information for large scale sequence analysis and visualization. The purpose of this research was to make OU statistical analysis available as a novel web-based tool for functional genomics and annotation. The tool is also available as a downloadable package. Results: The SeqWord Genome Browser (SWGB) was developed to visualize the natural compositional variation of DNA sequences. The applet is also used for identification of divergent genomic regions both in annotated sequences of bacterial chromosomes, plasmids, phages and viruses, and in raw DNA sequences prior to annotation by comparing local and global OU patterns. The applet allows fast and reliable identification of clusters of horizontally transferred genomic islands, large multi-domain genes and genes for ribosomal RNA. Within the majority of genomic fragments (a...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Hamilton Ganesan, Anna S. Rakitianskaia, Colin F. Davenport, Burkhard Tümmler, Oleg N. Reva
• Keywords: BMCBI 2008, Dna Sequences, Et Al, Genomic