Database Setup

Files required

1) Loci table (tab-delimited); columns need:

• Taxon_ID
• Taxon_Name
• Subtype*
• Locus_Start
• Locus_End
• Operon_Start*
• Operon_End*
• Array_Start*
• Array_End*
• Array_status**
• Operon_status***
• Genbank_file
• Array_File*
• Fasta_File*
• Author
• File_Creation_Date*

"*" blank values allowed

"**" Possible values: "present", "absent"

"***" Possible values: "intact", "absent", "broken", "shuffled"

"broken" = some genes missing "shuffled" = gene order

This table can easily be made in Excel and then saved as a tab-delimited file. Example:

loci excel

2) Array table files (tab-delimited; copy and paste from CRISPRFinder); columns needed:

• Start position
• Direct repeat sequence
• Spacer sequence
• End position

3) Genbank files for each organism of interest

4) Fasta files of each genome (only needed genome sequence information is not included in the genbank files).

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Directory setup

The directory name for this example: './CLdb/' The example loci table: 'loci.txt'

$ mkdir CLdb
$ cd CLdb
$ mkdir genbank

• place/symlink genbank files in this directory

$ mkdir array

• place/symlink array files in this directory