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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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 <url>http://www.bi.up.ac.za/SeqWord/mhhapplet.php</url>.</p

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage-2

And n0_4mer:D were selected for the X, Y and Z axes, respectively. Every dot on the dot-plot corresponds to a genomic fragment selected by the sliding window. Dots are spread and coloured in accordance with their values of the selected statistical OU parameters. Information for each dot may be found by one of the following methods: i) information for a dot under the mouse pointed by the mouse is shown in the 'Message' bar; ii) double clicking a dot returns us to the 'Gene map' tab with the corresponding genomic fragment highlighted; iii) framing the dots and clicking the 'Get' button opens a new applet window with the information about all selected regions. In this example the genomic regions of LT2 () that correspond to horizontally transferred genetic elements were selected (see discussion in the text).<p><b>Copyright information:</b></p><p>Taken from "The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage"</p><p>http://www.biomedcentral.com/1471-2105/9/333</p><p>BMC Bioinformatics 2008;9():333-333.</p><p>Published online 7 Aug 2008</p><p>PMCID:PMC2528017.</p><p></p

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage-3

Ely. The genomic regions covering the giant gene for the surface protein SwmB [] were highlighted by entering the coordinates of this gene into the 'Mark loci by coordinates' dialog. The genomic regions enriched with i) housekeeping genes; ii) genes for ribosomal proteins; iii) vestigial genetic elements (comprising pseudogenes, transposons, prophages and IS-elements) are indicated.<p><b>Copyright information:</b></p><p>Taken from "The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage"</p><p>http://www.biomedcentral.com/1471-2105/9/333</p><p>BMC Bioinformatics 2008;9():333-333.</p><p>Published online 7 Aug 2008</p><p>PMCID:PMC2528017.</p><p></p

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage-0

Ing category and use the interactive letters at the top to scroll the list to a sequence of interest.<p><b>Copyright information:</b></p><p>Taken from "The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage"</p><p>http://www.biomedcentral.com/1471-2105/9/333</p><p>BMC Bioinformatics 2008;9():333-333.</p><p>Published online 7 Aug 2008</p><p>PMCID:PMC2528017.</p><p></p

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage-1

Ws discrimination of divergent genomic regions. In this example a part of the chromosome of KT2440 (127–774 kbp) is displayed in the applet window. A genomic fragment was highlighted using the function 'Select region' and a giant gene, PP0168, was selected by 'Select gene'. A pop-up window 'Gene Details' was opened by double-clicking the gene on the map. Genes are indicated by red and grey (for hypotheticals) bars. The black horizontal line separates genes by their direction of translation.<p><b>Copyright information:</b></p><p>Taken from "The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage"</p><p>http://www.biomedcentral.com/1471-2105/9/333</p><p>BMC Bioinformatics 2008;9():333-333.</p><p>Published online 7 Aug 2008</p><p>PMCID:PMC2528017.</p><p></p

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage-6

Ing category and use the interactive letters at the top to scroll the list to a sequence of interest.<p><b>Copyright information:</b></p><p>Taken from "The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage"</p><p>http://www.biomedcentral.com/1471-2105/9/333</p><p>BMC Bioinformatics 2008;9():333-333.</p><p>Published online 7 Aug 2008</p><p>PMCID:PMC2528017.</p><p></p

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage-7

Ws discrimination of divergent genomic regions. In this example a part of the chromosome of KT2440 (127–774 kbp) is displayed in the applet window. A genomic fragment was highlighted using the function 'Select region' and a giant gene, PP0168, was selected by 'Select gene'. A pop-up window 'Gene Details' was opened by double-clicking the gene on the map. Genes are indicated by red and grey (for hypotheticals) bars. The black horizontal line separates genes by their direction of translation.<p><b>Copyright information:</b></p><p>Taken from "The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage"</p><p>http://www.biomedcentral.com/1471-2105/9/333</p><p>BMC Bioinformatics 2008;9():333-333.</p><p>Published online 7 Aug 2008</p><p>PMCID:PMC2528017.</p><p></p