“…The base-pairing probability matrix (BPPM) of an RNA sequence, which stores all the probabilities for possible base pairs in an RNA sequence (see Section 2 for the detailed definition), has played an essential role in a number of algorithms in RNA informatics, including RNA (common) secondary structure predictions (Seemann et al, 2008,) Lu et al, 2009;Hamada et al, 2009bHamada et al, , 2011cSato et al, 2011, multiple alignment of RNA sequences (Hofacker et al, 2004;Katoh and Toh, 2008;Hamada et al, 2009a;Sahraeian and Yoon, 2011), RNA-RNA interaction predictions (Kato et al, 2010;Seemann et al, 2011), RNA motif search (Hamada et al, 2006), and miRNA gene finding (Terai et al, 2007) (Wei et al, 2011). Estimating accurate base-pairing probabilities, therefore, has the potential to improve those algorithms without modifying them.…”