Welcome to the Loraine Lab QuickLoad server at the North Carolina Research Campus.

The data available via this site are designed for visualization in the Integrated Genome Browser.

Please use this site as a guide for how to set up a Quickload site for visualization in IGB. Contact Ann Loraine (aloraine -- at --- uncc.edu) if you have suggestions, questions, or corrections.

For information about the Loraine lab, visit http://www.transvar.org.

 Name                       Last modified      Size  Description
 Parent Directory                                -   
 A_thaliana_Apr_2008/       21-Sep-2009 20:22    -   Arabidopsis thaliana TAIR8 genome release
 A_thaliana_Jan_2004/       15-Jun-2009 12:02    -   Arabidopsis thaliana TIGRv5/TAIR7 genome release
 A_thaliana_Jun_2009/       19-Jul-2010 13:20    -   Arabidopsis thaliana TAIR9 genome release
 D_discoideum_Ax4_May_2009/ 22-Jul-2010 08:59    -   Dictyostelium discoideum strain Ax4 May 2009 genome
 contents.txt               19-Jul-2010 11:54  244   Available genome assemblies
 favicon.ico                31-Jul-2009 11:40  894   Icon IGB displays for this data source in the Data Access tab

A Quickload site can be located on the Web or on your local file system. It just needs to contain some basic files describing your genome and follow a simple structure, as follows. Other documentation is located on the IGB wiki: About QuickLoad.

contents.txt: This file lists the genome versions your Quickload will contain. Put this file at the top level of your Quickload directory - the Quickload data root. The first column gives the folder (directory) name for each genome version, and the second column specifies the genome's title that will appear above the data display in IGB. Here is an example. To ensure that IGB will display the latest release first, use the naming convention G_species_mon_yyyy, for example, O_sativa_Jun_2009, where G is the first letter of the genus, species is the species, month is a three letter abbreviation of the month (English) and yyyy is the year of the release.

mod_chromInfo.txt: This simple file should contain a list of all the chromosomes (or contigs) your finished or partially assembled genome contains. It should have two columns of data, separated by tabs. The first column lists the names of the chromosomes (or contigs), and the second column lists their sizes, in base pairs. For each genome, create a mod_chromInfo.txt file and place it in that genome's subdirectory in your Quickload data root. Here is an example from the Arabidopsis genome.

favicon.ico: This is a small image file IGB will display next to your data source in the Data Access panel. It is optional. To find out more about favicon.ico (short for favorites icon) read this wikipedia entry.

Genome data directories: Put your annotation and sequence files into subdirectories for each genome version you want to support. The name of the genome data directory should match the first column from your contents.txt file.

annots.xml: Each genome data directory should contain an annots.xml file that lists all the annotation files you want to make available via Quickload. For an example, see the annots.xml file for the TAIR9 genome annotations. List each data set using the "file" tag, which should have these attributes:

1. name - name of the file (e.g., TAIR9_mrna.bed.gz)
2. title - the data set title, this appears in the Data Access Panel
3. description - the text for the tooltips IGB will display about the data set
4. url - link to a Web page that has more information about the data set [optional]

Annotation data files. Put annotation files for each genome in that genome's data directory. IGB supports many formats. For gene models, use bed, following this example (TAIR9_mRNA.bed.gz) for protein-coding genes and this other example (TAIR9_miRNA.bed.gz) for non-coding genes. For EST or mRNA alignments, use psl which is the output from Jim Kent's blat alignment tool.

Sequence data files. For sequence, use bnib, a binary format that speeds up loading sequence data into the viewer. The name of each sequence should match the name of the chromosomes listed in the mod_chromInfo.txt file. For example, if the mod_chromInfo.txt file contains a sequence named contig123, then the corresponding sequence file should be named contig123.bnib.

To create a bnib file, you can use code from the Genoviz project and convert a fasta format file to the binary bnib format. Read the documentation How to create binary sequence files in BNIB format.

Note: If the only source for sequence data comes from Quickload, you won't be able to use the "Load Sequence in View" button in IGB's Data Access Panel. Just the "Load All sequence" button will work.