Weekly RNA News - Week XXXIV - September 2011

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs
Jan Gorodkin and Ivo L. Hofacker
PLOS Comp. Bio. 7, e1002100 (2011)

This is one of those cases where an article defies the traditional classification. By this I mean that although this article is clearly a review, it is not being published in a review journal, or maybe it's more likely that I don't understand the format of how PLoS works, for example their dislike for the traditional page-numbering scheme.
OK, stop ranting about irrelevancies and stick to the article.
Ohh, well, I can't stop with the "irrelevancies".
I guess it's the model of PLoS which makes articles hard to read, yes, an unfair judgement based on one article which you were expecting to be great (due to the authors) and then you're thoroughly deceived by the many errors and the lack of depth of the content, specially when compared with their much nicer article "De novo prediction of structured RNAs from genomic sequences" published in Trends in Biotechnology, a "regular" type of journal without the PLoS hype.

The article main topic is that of "de novo" discovery of non-coding RNA's. To this end the authors highlight two main strategies.

1) Sequence based alignments.
2) Synteny/Orthology with structure realignment.

Strategy one doesn't need much explanation, just that databases of know RNA sequences are necessary to make comparisons across organisms, for example the Rfam (RNA-families) database.
The second case brings up jargon, and it's not clear what they might mean if one sticks to the wikipedia definition of the term synteny. It would be nice if there was an example of what they mean in practice. What I understand is that perhaps in the second strategy secondary structure alignments are taken into account in the context of distant regions in the same chromosome which might refer to the "same" gene.


BlastR—fast and accurate database searches for non-coding RNAs
Giovanni Bussotti and Emanuele Raineri and Ionas Erb and Matthias Zytnicki and Andreas Wilm and Emmanuel Beaudoing and Philipp Bucher and Cedric Notredame
Nucleic Acids Research, 39, 6886-6895 (2011)

The main idea of this article is to use the already existing techniques for alignments of proteins to the alignment of RNA's. To test the perl script they have implemented to interact with the already existing ncbi-blast package I downloaded the full long-non-coding RNA database from :
http://www.lncrnadb.org/
And then I used it as database to compare, say, one of the sequences existing in such database.
Not surprisingly the result is a 100% score in their similarity measure, and it took a couple of hours to get it all done. Here's a snapshot of the results of running the command:

blastallR.pl -p blastr -i NR_003141.3 -d database/ncbi_blastR_format/db -m 8

Not surprisingly the first score matches as indicated by the 100% score.