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. 2012 May 23;13:202.
doi: 10.1186/1471-2164-13-202.

Comparing Thousands of Circular Genomes Using the CGView Comparison Tool

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Free PMC article

Comparing Thousands of Circular Genomes Using the CGView Comparison Tool

Jason R Grant et al. BMC Genomics. .
Free PMC article

Abstract

Background: Continued sequencing efforts coupled with advances in sequencing technology will lead to the completion of a vast number of small genomes. Whole-genome comparisons represent an important part of the analysis of any new genome sequence, as they can provide a better understanding of the biology and evolution of the source organism. Visualization of the results is important, as it allows information from a variety of sources to be integrated and interpreted. However, existing graphical comparison tools lack features needed for efficiently comparing a new genome to hundreds or thousands of existing sequences. Moreover, existing tools are limited in terms of the types of comparisons that can be performed, the extent to which the output can be customized, and the ease with which the entire process can be automated.

Results: The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG (Clusters of Orthologous Groups of proteins) category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation.

Conclusion: CCT can be used to visually compare a reference sequence to thousands of existing genomes or sequence collections (next-generation sequencing reads for example) on a standard desktop computer. It provides analysis and visualization functionality not available in any existing circular genome visualization tool. By visually presenting sequence conservation information along with functional classifications and sequence composition characteristics, CCT can be a useful tool for identifying rapidly evolving or novel sequences, horizontally transferred sequences, or unusual functional properties in newly sequenced genomes. CCT is freely available for download at http://stothard.afns.ualberta.ca/downloads/CCT/.

Figures

Figure 1
Figure 1
CCT map comparing an E. coli reference sequence to other E. coli genomes. This map was generated by commands 1 to 5 given in Additional file 1A. Starting from the outermost ring the feature rings depict: 1. COG functional categories for forward strand coding sequences; 2. Forward strand sequence features; 3. Reverse strand sequence features; 4. COG functional categories for reverse strand coding sequences. The next 30 rings show regions of sequence similarity detected by BLAST comparisons conducted between CDS translations from the reference genome and 30 E. coli comparison genomes. The last two rings display the GC content and GC skew.
Figure 2
Figure 2
Zoomed CCT map showing enhanced detail. This 15X zoomed map was produced by command 6 given in Additional file 1A. Starting from the uppermost slot the feature slots depict: 1. COG functional categories for forward strand coding sequences; 2. Forward strand sequence features; 3. Reverse strand sequence features; 4. COG functional categories for reverse strand coding sequences. The next 30 slots show regions of sequence similarity detected by BLAST comparisons conducted between CDS translations from the reference genome and 30 E. coli comparison genomes. The last two slots show the GC content and GC skew.
Figure 3
Figure 3
CCT map comparing the rat mitochondrial genome to itself and 99 other mitochondrial genomes. This map was generated by commands given in Additional file 2A. Starting from the outermost ring the feature rings depict: 1. COG functional categories for forward strand coding sequences; 2. Forward strand sequence features; 3. Reverse strand sequence features; 4. COG functional categories for reverse strand coding sequences (the ring is empty because no COG categories were assigned). The remaining rings show regions of sequence similarity detected by BLAST comparisons conducted between CDS translations from the reference genome and 100 comparison genomes.
Figure 4
Figure 4
Montage of CCT maps comparing nine Rickettsia genomes. A montage of maps comparing Rickettsia genomes at the protein level, created using the build_blast_atlas_all_vs_all.sh script. The montage is comprised of nine separate CCT maps, each depicting one of the genomes as the reference and the remaining eight as the comparison genomes. Starting from the outermost ring the four features rings depict: 1. COG functional categories for forward strand coding sequences; 2. Forward strand sequence features; 3. Reverse strand sequence features; 4. COG functional categories for reverse strand coding sequences. The remaining rings show regions of similarity detected using BLAST (blastp).

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