Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.

ABSTRACT: Secondary structures of ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Experimental observations and computing limitations suggest that we can approach the secondary structure prediction problem for long RNA sequences by segmenting them into shorter chunks, predicting the secondary structures of each chunk individually using existing prediction programs, and then assembling the results to give the structure of the original sequence. The selection of cutting points is a crucial component of the segmenting step. Noting that stem-loops and pseudoknots always contain an inversion, i.e., a stretch of nucleotides followed closely by its inverse complementary sequence, we developed two cutting methods for segmenting lon

SUBMITTER: Yehdego DT 

PROVIDER: S-EPMC4444072 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature