An Easy-On-The-Eye Genome Browser 

To cite: Ganesan H, Rakitianskaia AS, Davenport CF, Tümmler B, Reva ON. The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. BMC bioinformatics 9 (1), 333.

The SeqWord Genome Browser (SWGB) was developed to visualize the natural compositional polymorphism of DNA sequences by analysis of local oligonucleotide usage (OU) pattern signatures. 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 multidomain genes, non-coding sequences 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.

Several informative OU statistical parameters (D, PS, RV, GRV, GC and GCS) were calculated for local OU patterns to facilitate prediction of gene classes. A database of pre-calculated OU patterns determined for 8 kb long overlapping fragments of bacterial chromosomes with a step of 2 kb was developed. Alternatively, a standalone program for deriving data (OligoWords) and a local version of the Genome Browser are available to analyse your own DNA sequences locally.

To analyze a genome of interest try the following steps:

1. Select the radio button of a genome of interest;

2. Click the button ‘Display in the Applet’. The genomic map of the selected microorganism will be displayed on the ‘Gene Map’ tab of the applet window.

3. Loci of structural perturbations of chromosomal DNA may be identified visually on the map.

·        To change the scale of the map, select a value from 0.1 to 10 in the ‘Zoom’ counter and click ‘Enter’.

·        To get information about a gene, move the mouse pointer over the gene bar on the map and read the description in the ‘Message’ field. Or click the gene to open the ‘Gene Details’ window.

·        To highlight a genomic region, choose Tools->Select Region, enter the coordinates of the region in the dialog and press ‘Ok’. To remove highlighting, choose Tools->Clear selection.

·        To display a genomic region in the applet window, choose Tools->Zoom into region, enter the coordinates of the region in the dialog and press ‘Ok’. To remove the zoom, choose Tools->Clear zoom.

·        To highlight a gene on the map, click the button ‘Select Gene’, sort the genes in the dialog by names, functions or coordinates, and click ‘Ok’. To remove highlighting, click the button ‘Clear Gene Selection’.

4. To reach all values of all OU statistical parameters calculated for a given genome, select File->Export. A new window will open with the current dataset in text format. To save the genome dataset locally, select File->Save as text. In the future this file may be opened in the applet by the File->Open command.

5. The tab ‘Diagram’ provides tools to analyze statistics of the distribution of OU parameters and to automatically retrieve the genomic loci of different functional categories. 

·       Select a parameter for the axis X or Y and click ‘Enter’. The program shows a histogram of distribution of the parameter’s values among genomic loci. The ‘Statistical Data’ panel reads arithmetic average, standard deviation, skew and inner quartiles values of the distribution. To show the mean value and quartiles, set corresponding checkboxes. To change the number of columns in the histogram, select the appropriate value in the counter ‘'# bars’ and click ‘Enter’.

·        To analyze distributions of several OU statistical parameters at the same time, choose appropriate values in the combo boxes ‘X axis’, ‘Y axis’ and ‘Z axis’. Click ‘Enter’. The program shows a dot-plot matrix where each dot corresponds to an 8 kb long genomic fragment.

·        To filter the genomic fragments by the third parameter, select a part of the color bar you want to display using the mouse pointer . To cancel filtering, double click the grey part of the color bar.

·        Filtering may be performed with all available parameters, not only those that were selected for axes X, Y and Z. To set up filtering, click the button 'Filter' and in the dialog that pops up set the minimal and maximal values of any parameters of interest. Click 'OK'. The dots of the genomic fragments with values outside of the set thresholds will be removed from the dot plot. To cancel filtering, open the 'Filter' dialog again and move all left sliders to the far left position, and all right sliders to the far right position. Click 'OK'.

·        Using the mouse, draw a box around a group of dots on the plot and click ‘Get’. The program returns a list of genomic loci represented by the outlined dots. Overlapping genomic fragments will be automatically concatenated and the coordinates of the loci in the list are accompanied with the annotation information of the constituent genes.

·        Double clicking a dot on the plot redirects us back to the ‘Gene Map’ tab where the corresponding genomic fragment will be highlighted.

·        Click the button ‘Mark’ and in the dialog enter the coordinates of genomic fragments of interest (coordinates of several fragments may be added to the list). Click ‘Ok’. The corresponding dots on the dot-plot will be highlighted. To remove highlighting and/or the selector frame, click the button ‘Clear’.

The SeqWord Genome Browser in action

Several procedures for semi-automatic identification of horizontally transferred genomic islands; ribosomal gene clusters; long multidomain genes and non-coding sequences and pseudogenes are proposed.