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. 2011 Oct 26;6(10):e25642. doi: 10.1371/journal.pone.0025642

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© 2011 Mysara et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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MysiRNA-Designer takes an accession; get the mRNA sequence from NCBI-GenBank. Finds out if this mRNA has other transcript(s), performs multiple sequence alignment with the transcripts, if any, and takes the consensus un-gapped sequence, designs all possible siRNA in targeting sequence space available; performs target accessibility evaluation selection siRNA with energetically and structurally favored siRNA-mRNA binding. Predict siRNA efficiency using the implemented multi-score filtration; select the candidates that pass the threshold assigned for each of the ten tools used, eliminates siRNA targeting SNPs regions or off-targeted mRNA, either complete or seed homology off-target. Finally, MysiRNA-Designer shows the accepted candidates with the predicted silencing efficiency using MysiRNA-Model, it filters candidates above the assigned threshold, as the user requires.