Gas station without pumps

2014 September 30

Ebola genome browser

Filed under: Uncategorized — gasstationwithoutpumps @ 21:00
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For the past week, I’ve been watching the genome browser team (led by Jim Kent) scramble to get together an information resource to aid in the fight against the Ebola virus.  They went public today:

We are excited to announce the release of a Genome Browser and information portal for the Jun. 2014 assembly of the Ebola virus (UCSC version eboVir3, GenBank accession KM034562) submitted by the Broad Institute. We have worked closely with the Pardis Sabeti lab at the Broad Institute and other Ebola experts throughout the world to incorporate annotations that will be useful to those studying Ebola. Annotation tracks included in this initial release include genes from NCBI, B- and T-cell epitopes from the IEDB, structural annotations from UniProt and a wealth of SNP data from the 2014 publication by the Sabeti lab. This initial release also contains a 160-way alignment comprising 158 Ebola virus sequences from various African outbreaks and 2 Marburg virus sequences. You can find links to the Ebola virus Genome Browser and more information on the Ebola virus itself on our Ebola Portal page.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The Ebola virus (eboVir3) browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release and the conditions for use of these data.

Matthew Speir
UCSC Genome Bioinformatics Group

2011 June 17

Giant viruses

Filed under: Uncategorized — gasstationwithoutpumps @ 07:45
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American Scientist has a nice overview article on Giant Viruses, viruses as big as bacterial cells, with as many genes.  Mimivirus, for example, has a 1.2 megabase genome, with 1018 genes, and has a diameter of 750 nm. OK, that’s an extreme example—the biggest known—but there are several giant viruses, defined as having a diameter of 200 nm or more and a genome of 300 kbase or more.  Mimivirus is big not just because of its large genome.  The capsid proper is only about 500n, across (still huge), but it is also covered with a layer of closely packed fibers that may be related to collagen.  So far, mimivirus is the only known giant virus to have this fiber coat.

The usual technique for separating viruses from cells is filtration with a 200nm filter, so giant viruses are pretty much defined as those that get missed by the usual separation technique (like artificial intelligence is facetiously defined as those things we’d like to do on a computer, but don’t know how to).  There is a project I’ve been loosely associated with to extract viral genes from salt ponds, and I’m now wondering whether there are any giant viruses among the halophiles—they won’t have been evident in the viral fraction that was sequenced.

There is some hope for finding evidence of giant viruses, though, even in the current metagenomic data.  It turns out that giant viruses have viruses that infect them (called virophages).  Although viral satellites have been known for a while (small bits of nucleic acid that hitchhike in the viral capsids and rely on them for replication), a giant virus found in 2008 (called mamavirus) has a satellite (called Sputnik) that interferes with the infectivity of mamavirus.  Other vibrophages have been found since.

There is a sidebar to the article on giant viruses (hidden behind a tree of DNA replication genes) that discusses the current controversy over whether viruses are alive. Personally, I favor Jean-Michel Claverie’s statement, “I believe that the virus factory should be considered the actual virus organism when referring to a virus. Incidentally, in this interpretation, the living nature of viruses is undisputable, on the same footing as intracellular bacterial parasites.” If you view the reproductive machinery as the organism, and the virion as an intermediate form (like bacterial cysts or fungal spores), then viruses fit fairly comfortably in the spectrum of living things, at the extreme end of parasites that can’t live without hosts.  This seems to me a much more reasonable position than one that insists that living things must fit on the mystical “tree of life”.



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