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For example, there are two Oryza sativa (rice) subspecies in wide cultivation: japonica and indica.The first rice sequence published was from the Nipponbare variety which is a member of the japonica subspecies. Because an indica genome sequence is now available, we need names that distinguish them. We designate assemblies of the japonica genome sequence using prefix O_sativa_japonica and the month and year of release: O_sativa_japonica_Jun_2009. Annotations and sequence data reside in genome version folder O_sativa_japonica_Jun_2009 on the main IGB QuickLoad site - view its contents by visiting http://igbquickload.org/quickload/O_sativa_japonica_Jun_2009

Tip: If you set up your QuickLoad site in the Web directories of an Apache server, you can modify and fine-tune how files are displayed by adding directives to the .htaccess file in that directory.  You can configure Apache to allow users to view the contents of your QuickLoad directory and include a short description of each file or data set. Here is an example:

Step Three: Create contents.txt file.

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• View contents.txt on IGB QuickLoad: http://igbquickload.org/quickload/contents.txt

Note: You can include other directories and other files in your QL site folder;  IGB will simply ignore anything that isn't listed in your contents.txt file. Also, any changes in the name of the genome directory must be updated in the contents.txt file or IGB will not recognize it.

Optional Step: Create a synonyms.txt file.

This is a list of synonyms for genomes. This list allows you to match names across different QuickLoad sites and also the Galaxy workflow site. For example, if a QuickLoad site at another location uses different names to refer to the same genome version, you can specify these in the synonyms.txt. Each line contains any number of synonyms for a genome, separated by tabs.

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Here is an example*: *http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt

Note: You can create your genome.txt file from a sequence 2bit file (see below) using twoBitInfo, available from http://hgdownload.cse.ucsc.edu/admin/exe/. See Step Seven: Add sequence data.

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Each line contains:  CONTIG_START tab CONTIG_NAME tab CONTIG_LENGTH tab CHROMOSOME_NAME tab CHROMOSOME_LENGTH

Note: This is a relatively old feature in IGB and we are not entirely sure it still works.

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$ faToTwoBit A_thaliana_Jun_2009.fa A_thaliana_Jun_2009.2bit

Note: The 2bit sequence file should have the same name as your genome version directory and should have file extension "2bit," e.g., A_thaliana_Jun_2009.2bit.

However, before you create the sequence files, check that the names of sequences in your fasta file match the names used in your annotation files. For example, if your annotations file lists sequence name chr1, then the fasta file should contain a sequence record with fasta header ">chr1" and nothing else. If they don't match, you'll need to either edit your fasta headers or create a sequence synonyms files.

Note: You can make your genome.txt file (Step Four above) using twoBitInfo, another program available from http://hgdownload.cse.ucsc.edu/admin/exe/. To create a genome.txt file from a 2bit sequence file, do something like this:

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