Details

Autor(en) / Beteiligte

• Rampášek, Ladislav
• Jimenez, Randi M
• Lupták, Andrej
• Vinař, Tomáš
• Brejová, Broňa

Titel

RNA motif search with data-driven element ordering

Ist Teil von

• BMC bioinformatics, 2016-05, Vol.17 (1), p.216-216, Article 216

Ort / Verlag

England: BioMed Central Ltd

Erscheinungsjahr

2016

Link zum Volltext

Quelle

SpringerLink (Online service)

Beschreibungen/Notizen

• In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .