Non-coding RNA prediction and functional filtering using pentamer sequence motifs

Non-coding RNAs play important roles in the cell; one prominent example is the regulation of gene expression via establishment of stable joint structures with target mRNAs. Sequence motifs are also important determinants of ncRNA structure. In this thesis we introduce two computational methods that exploit differential distributions of short sequence motifs in (long) ncRNAs for the purpose of identifying their loci and potential regulatory roles: (1) smyRNA is an ab initio ncRNA gene finder which is based on identification of sequence motifs that have potential structural roles on a genome sequence and (2) pRuNA is an index structure which can search a collection of ncRNAs to determine those that can establish stable interactions with a query mRNA. It uses differential distribution of sequence motifs with potential functional roles for the purpose of pruning out a significant majority of the ncRNAs while retaining the actual regulatory RNAs of a query mRNA.