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...w size of 80 nucleotides (nt) and a maximum base pair span of 40 nt, were subsequently used as standard values for local secondary structure predictions (14,22,24). Similar analyses were performed in =-=(20,36)-=-. A window size that was equal to the maximum base pair span was used in (33) and it is also the default setting in RNAplfold. Our benchmark analysis showed that these previously used parameters perfo...

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... Folding constraints such as maximum nucleotide distance L for two bases to form a pair can be imposed for "local" folding. Such local folding was found to be significant for prokaryotic applications =-=[29]-=-. For prokaryotes, transcription and translation are tightly coupled events so that the target mRNA is unlikely to be able to fold globally. In contrast, eukaryotic mRNAs are first transcribed in nucl...

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...mproved predictions for structural RNAs [35]. Not surprisingly, predictions by Sfold significantly correlate with experimental results in gene down-regulation studies using antisense oligonucleotides =-=[36, 37]-=-, RNAi [38], or microRNAs [25]; in contrast, a lack of significant correlation was found in these applications for predictions based on free energy minimization. Here, we explore the potential value o...

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...eavage sites. ODN inhibition efficiency can also be tested in in vitro transcription/translation experiments, in which the amount of expressed gene product is quantified following incubation with ODN =-=[14,17]-=-. RNA secondary structure predictions can be carried out by computer-assisted free energy minimization programs (like Mfold [18]) or structure sampling algorithms (like Sfold [19]) (for reviews see [2...

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...08). In these cases, several computational methods have been proposed and found to be effective at predicting the relevant target sites (Ding and Lawrence 2001; Wang and Drlica 2004; Far et al. 2005; =-=Shao et al. 2006-=-; Tafer et al. 2008; Backofen and Hess 2010; Thomas et al. 2010). One recurring theme is the use of RNA secondary structure prediction algorithms to calculate the free energy changes, DGbind, associat...

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...w size of 80 nucleotides (nt) and a maximum base pair span of 40 nt, were subsequently used as standard values for local secondary structure predictions (14,22,24). Similar analyses were performed in =-=(20,36)-=-. A window size that was equal to the maximum base pair span was used in (33) and it is also the default setting in RNAplfold. Our benchmark analysis showed that these previously used parameters perfo...

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...y predicted. For longer RNAs, such as in trans-splicing when the IGS and splice site are on different molecules, target accessibility is extremely important and can be predicted with tools like Sfold =-=[136]-=-. Just as in the random selection method, the functional effect of a splice site is not typically included in the prediction. Depending on the quality of the computational prediction, the chosen splic...