Genom is a tool for calculating the number of the genes in synteny blocks between two prokaryotic genomes. It uses the table generated by GeneOrder4.01. GeneOrder4.0 is a tool for performing comparative analysis of gene order and synteny in genomes. It presents genome comparisons between two organisms as a table, listing the order of similar genes. Using this table in Excel, we generate such a .csv file which serves as input file for Genom. The application takes those synteny blocks into account where at least two genes are in the same order. It counts these genes and as a result we get the number of genes with the same order between two prokaryotic genomes.
The input file should be in .CSV format. The file contains two columns. It could be created using the output file obtained by GeneOrder4.0
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Open the Output file of GeneOrder4.0 in Excel
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Delete columns C and D
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Delete row one
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Select entire columns A and B
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Use command Replace
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Find what: (*) Replace with: leave blank
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We get data in two columns
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Save the data as a .csv file
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This is the input file for Genom
Using the program
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Use the button with letter G after opening the application to start the program
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Select a created csv file
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Using buttons “convert it”, “analize it”, “look at the result” the Genom calculates the number of genes in synteny blocks between two prokaryotic genomes
Video tutorial
1Mahadevan P. and Seto D. 2010. Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0. BMC Research Notes 3:41.
