Adding a new genome - X. tropicalis Nov 2009

Introduction

An IGB user contacted us with a request to add a new genome to the IGB QuickLoad system - the Xenopus tropicalis genome assembly dated November, 2009, also called JGI 4.2/xenTro3. (See: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=262072157&clade=vertebrate&org=X.+tropicalis&db=0).

Because this genome is supported at the UCSC Genome Browser, adding it to the system should be fairly straightforward. All we need to do is download the data, format it, and move it onto the main IGB QuickLoad site currently hosted at UNC Charlotte, in the Bioinformatics and Genomics Department's server room.

Methods

Step one is to download the sequence data.

The UCSC Web site provides this page that lists the different organisms supported in their system. I followed the link to the X. tropicalis genome and clicked the link labeled Full data set, which took me to the "bigZips" page here: http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/bigZips/.

Fortunately, it appears that UCSC already provides the fasta sequence data in 2bit format, saving me a step.

First, I added a new directory for this genome to my checked-out copy of the IGB QuickLoad subversion repository, like so:

Next, I changed in the new directory and then downloaded this 2bit file using wget in the usual way:

Once the file downloaded, I used twoBitInfo to make a "genome.txt" file reporting the names of the assembled chromosomes and contigs and their sizes.

Next, I used the UCSC Table Browser to get the RefSeq genes for this species. Here are the settings I used:
Unfortunately, there don't appear to be a lot of RefSeq gene annotations available for this species:

Probably it would be a good idea to look for another data set that might provide a more complete view of the Xenopus expressed gene repertoire.

Using the Table Browser, I explored the available data sets for Xenopus:

svn add

To be continued.....