Bioinformatický seminár

Tue 13 Mar. 2012, 17:20
I-9

Title: Weinberg, Breaker (2011) R2R - software to speed the depiction of aesthetic consensus RNA secondary structures
Speaker: Pali Kmeč

BACKGROUND: With continuing identification of novel structured noncoding
RNAs, there is an increasing need to create schematic diagrams showing the
consensus features of these molecules. RNA structural diagrams are
typically made either with general-purpose drawing programs like Adobe
Illustrator, or with automated or interactive programs specific to RNA.
Unfortunately, the use of applications like Illustrator is extremely time
consuming, while existing RNA-specific programs produce figures that are
useful, but usually not of the same aesthetic quality as those produced at
great cost in Illustrator. Additionally, most existing RNA-specific
applications are designed for drawing single RNA molecules, not consensus
diagrams. RESULTS: We created R2R, a computer program that facilitates the
generation of aesthetic and readable drawings of RNA consensus diagrams in
a fraction of the time required with general-purpose drawing programs.
Since the inference of a consensus RNA structure typically requires a
multiple-sequence alignment, the R2R user annotates the alignment with
commands directing the layout and annotation of the RNA. R2R creates SVG
or PDF output that can be imported into Adobe Illustrator, Inkscape or
CorelDRAW. R2R can be used to create consensus sequence and secondary
structure models for novel RNA structures or to revise models when new
representatives for known RNA classes become available. Although R2R does
not currently have a graphical user interface, it has proven useful in our
efforts to create 100 schematic models of distinct noncoding RNA classes.
CONCLUSIONS: R2R makes it possible to obtain high-quality drawings of the
consensus sequence and structural models of many diverse RNA structures
with a more practical amount of effort. R2R software is available at
http://breaker.research.yale.edu/R2R and as an Additional file.