The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
Open Access
- 7 August 2008
- journal article
- software
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 9 (1), 333
- https://doi.org/10.1186/1471-2105-9-333
Abstract
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 (also termed genomic core sequence), regions enriched with housekeeping genes, ribosomal proteins and the regions rich in pseudogenes or genetic vestiges may be contrasted. Conclusion The SWGB applet presents a range of comprehensive OU statistical parameters calculated for a range of bacterial species, plasmids and phages. It is available on the Internet at http://www.bi.up.ac.za/SeqWord/mhhapplet.php.Keywords
This publication has 32 references indexed in Scilit:
- Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomesBMC Genomics, 2008
- HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selectionNucleic Acids Research, 2007
- Contribution of Horizontally Acquired Genomic Islands to the Evolution of the Tubercle BacilliMolecular Biology and Evolution, 2007
- SwmB, a 1.12-Megadalton Protein That Is Required for Nonflagellar Swimming Motility in SynechococcusJournal of Bacteriology, 2007
- Use of Artificial Genomes in Assessing Methods for Atypical Gene DetectionPLoS Computational Biology, 2005
- Application of tetranucleotide frequencies for the assignment of genomic fragmentsEnvironmental Microbiology, 2004
- Biased biological functions of horizontally transferred genes in prokaryotic genomesNature Genetics, 2004
- Informatics for Unveiling Hidden Genome SignaturesGenome Research, 2003
- Where are the pseudogenes in bacterial genomes?Trends in Microbiology, 2001
- Detecting Alien Genes in Bacterial GenomesaAnnals of the New York Academy of Sciences, 1999