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
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Last modified: 2006-04-21 14:49 kristin