The OpenHelix Blog

Just a few links for your reading pleasure from the last week.

While the mainstream news is reporting on the demise (redefinition) of the ‘gene‘, some high schools kids are doing amazing things with ‘genes.’

Oh, and if, like us, you can’t wait till the annual NAR database is published officially, you can always check out the advanced online publication of the articles to find new and updated databases (like the SpBase, sea urchin, database that went public earlier this year and SuperToxic, a database of over 60,000 toxic compounds) and genome resources!

In the recent database issue of NAR, there are two reports of transposable element (TE) databases. I already discussed one in an earlier post. That one is a database that includes Gypsy elements (non-LTR retroposons) and retroviruses and aims to be a database “devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements.” Hopefully to develop into a database of all TE’s. The other paper, by Levy et al. (“TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates“)¹, I’ll discus briefly here introduces a somewhat different database of transposable elements.

As the paper discusses, TE’s have been implicated in a large number of effects on the vertebrate genome: affecting expression and “contributing to genetic diversity, genomic expansion, genomic content and genomic rearrangements.” Whether these immense changes are the raison d’être for transposable elements or the byproduct of a parasitic DNA element, I’ll leave for discussion (though I would side with the latter), but they are unarguably major factors in genome evolution and don’t fit the definition of “junk DNA.” .

I started my Ph.D. studies into the evolution of non-LTR retrotransposable elements in 1990 and found the world of mobile genetic elements or transposons (aka a long time ago… jumping genes) to be varied, complicated and fascinating. In 1993 I discovered the web. I’ve hoped for and searched for a database of these “Mobile genetic elements [that] are self-contained genomic units capable of proliferating within their host genomes”¹ to little satisfaction. Such databases exist such as the Mouse Transposon Insertion Database and the dbRIP (human retrotransposon polymorphisms in humans) and several others. But these almost entirely organism-specific databases. This helps the study of the organism (mobile elements have an effect on the genome), but little in the study of transposons as a class.

So, I was happy to see the latest article in the NAR database issue on GypDB

I just finished reading this paper out this month in PNAS, “Specific expression of long noncoding RNAS.” From the looks of it, the paper has conjured up an interesting discussion in the science blogosphere surrounding the paper and the term “Junk DNA.” Before I get to that discussion, let me give a brief synopsis of and thoughts on the paper (and a link to a ncRNA database at the end).

For years I have been following the NAR database issue, watching the growth in the number of resources from a handful years ago to the hundreds lately. It is great to see what new resources have been added each year–there are people who are solving genomics problems in really creative ways.

Last year (2007) there were 968 resources listed, which was over a hundred more than the previous year (Galperin, Nucleic Acids Research, 2007, Vol. 35, Database issue D3-D4).I’m going to bet on over another hundred new ones this year, for a total of 1086.

Now I’m going over to look for new number in the advanced access section…. The Molecular Biology Database Collection: 2008 update and Michael Galperin reports on: 1078 databases. 110 more this year!

110…well, I will have to check them out and see who the new kids on the block are. I love new databases!