Bioinformatický seminár

Tue 23 Oct. 2012, 17:20

Title: Steffen Heyne et al. GraphClust: alignment-free structural clustering of local RNA secondarystructures
Speaker: Jaro Budiš

MOTIVATION: Clustering according to sequence-structure similarity has now become 
a generally accepted scheme for ncRNA annotation. Its application to complete
genomic sequences as well as whole transcriptomes is therefore desirable but
hindered by extremely high computational costs. RESULTS: We present a novel
linear-time, alignment-free method for comparing and clustering RNAs according to
sequence and structure. The approach scales to datasets of hundreds of thousands 
of sequences. The quality of the retrieved clusters has been benchmarked against 
known ncRNA datasets and is comparable to state-of-the-art sequence-structure
methods although achieving speedups of several orders of magnitude. A selection
of applications aiming at the detection of novel structural ncRNAs are presented.
Exemplarily, we predicted local structural elements specific to lincRNAs likely
functionally associating involved transcripts to vital processes of the human
nervous system. In total, we predicted 349 local structural RNA elements.
AVAILABILITY: The GraphClust pipeline is available on request.