The OpenHelix Blog

Welcome to our Friday feature link dump: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

• A great list of bioinformatics analysis algorithms and tools. [Trey]
• BMC has a new journal entitled Mobile DNA (and one of the editors-in-chief was my Ph.D. advisor, Thomas Eickbush). Some excellent first papers you should check out. [Trey]
• Interesting study on genetically engineered plants: “The impact of transgenes is basically limited to their immediate function” for the interview, paper is here. [Mary]
• Speaking of BMC, BMC Biology now incorporates the Journal of Biology (they had a ‘relaunch’ of the journal at the Experimental Biology conference, across the aisle from where we were.. cake, champagne and t-shirts! . Hey, check out the site for the free iPad giveaway. Funny, I counted 3 iPad giveaways in the exhibit hall.. [Trey]
• Found this as I was writing an article on informal education in bioinformatics for a special issue of Briefings in Bioinformatics. It is from NatureNews: “US seeks to make science free for all“   [Jennifer]
• Xenopus!  I always liked that name.  In fact, am now kicking self that I haven’t used that for some online persona….Anyway, Xenopus tropicalis, first amphibian sequence now available, see Science.  [Mary]

Today’s tip is on a TARGeT. TARGeT is, as the the paper’s title in the this year’s NAR’s issue states, “a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences.” There are several things you can do at TARGeT. Using BLAST, PHI BLAST, MUSCLE and TreeBest ,the main function of TARGeT is  to quickly obtain gene and transposon families from a query sequence. The tip today is a quick intro to the tool and a search on an R1 non-LTR transposon.

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.” .

A commenter, McBlawg’s Graham Steel, left a comment about Silobreaker as a possible search engine. Indeed, it is a pretty nice tool. It’s more general news than genomics , but I did a quick search on “transposon” and found this hilarious, and informative, video clip explaining how transpose rearranges parts of the genome. The video is done in the 50’s “Learning about Sex” style. For your viewing pleasure .

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).