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Introduction

IGB provides access to a wide variety of species and genome versions; the full list is Species currently recognized by IGB. However, you may want to establish your own genome version, or even work with a species not on the list. This page should help you get started. If you want to make your species/genome available to more than yourself, you can easily set up a Quickload site on your computer, which will utilize many of the following steps. Read about Creating QuickLoad Sites.

Naming a Genome

If you are building a genome for display in IGB, we recommend that you give it an IGB-friendly name, consisting of the month and year of release combined with genus and species, following the pattern: G_species_mon_yyyy, where G is the first letter of the genus, mon is the three-letter English abbreviation for the month the genome was released, and year is the year of the release. For example, A_thaliana_Jun_2009 is the Arabidopsis thaliana genome assembly and annotation published in June of 2009; or H_sapiens_Feb_2009 which is the Homo sapiens genome assembly published February of 2009. Using this scheme will ensure that IGB displays the latest genome first in the genome menu under the Data Access tab

Adding a Common Name for a Species

When users operate the pulldown menu to choose a species to view in IGB, a 'tool tip' message indicating the common name of the species appears.  If you are adding a new species, contact the IGB developers and ask to have your common name added to the species.txt file under version control at sourceforge.net. This is a tab delimited file that lists all the species that IGB supports, including common names for many of them.

Synonyms

Unfortunately, different groups tend to refer to the same genome or chromosome by different names.  For example, NCBI human genome build 35 is also known as hg17 and ensembl1834, as well as H_sapiens_May_2004.  When IGB is able to recognize that two names refer to the same genome or chromosome, it will merge the data.  Otherwise it will keep the two data sets distinct.  Currently, IGB uses a simple table of synonyms to store these associations.  You can create your own set of synonyms that will extend this set if needed.

These synonyms also cover the names of the chromosomes inside each of these assemblies. While some may refer to CHR1, or chr1, or chr 1, IGB can recognize that they refer to the same sequence when the synonyms files are properly updated. As a default, IGB is case-insensitive to the genome and chromosome names. The default synonyms also cover almost all genome versions up to date. If you need to add to the synonyms however, read about Personal Synonyms in the Data Sources Tab page.

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