Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 06-006


RNAstrand: Reading Direction of Structured RNAs in Multiple Sequence Alignments

Kristin Missal, Peter F. Stadler

Bioinformatics Application Note

Genome-wide screens for structured ncRNA genes in mammals, urochordates, and nematodes have predicted thousands of putative ncRNA genes and other structured RNA motifs. A prerequisite for their functional annotation is to determine the reading direction with high precision. While folding energies of an RNA and its reverse complement are similar, the difference are sufficient at least in conjunction with substitution patterns to discriminate between structured RNAs and their complements. We present here a support vector machine (SVM) that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment.

Keywords: ncRNA genes, reading direction, support vector machine

Return to 2006 working papers list.
Last modified: 2006-04-21 14:49 kristin