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Comparing thousands of circular genomes using the CGView Comparison Tool

Jason R Grant, Adriano S Arantes and Paul Stothard*

Author Affiliations

Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G2P5, Canada

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BMC Genomics 2012, 13:202  doi:10.1186/1471-2164-13-202

Published: 23 May 2012

Additional files

Additional file 1:

Example CCT workflow using the cgview_comparison_tool.pl script. (A) Commands for comparing a bacterial genome of interest, E. coli NRG857c (O83:H1), to all other E. coli genomes available in NCBI’s RefSeq collection. Note that these commands complete the entire map creation process, from downloading the sequence files to generating a regular and zoomed map in PNG format. (B) The directory structure of the CCT project created using the cgview_comparison_tool.pl command. The bold items are directories and the regular items are files.

Format: PDF Size: 104KB Download file

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Open Data

Additional file 2:

Example CCT workflow using the build_blast_atlas.sh script. A) Commands to create a BLAST atlas comparing the Rattus norvegicus mitochondrial genome to all mitochondrial genomes available in NCBI’s RefSeq collection. Note that by default the 100 most similar comparison genomes are selected by CCT after BLAST analysis for inclusion on the final map. B) The directory structure created by the build_blast_atlas.sh command. The bold items are directories and the regular items are files.

Format: PDF Size: 84KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data