PACCMIT-CDS / PACCMIT
PACCMIT-CDS is a software that finds potential microRNA targets within coding sequences by searching for conserved motifs that are complementary to the microRNA seed region and also overrepresented in comparison with a background model preserving both codon usage and amino acid sequence.
PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets) is a flexible algorithm that filters potential miRNA binding sites in 3’UTR regions by their conservation, accessibility, or both, and then ranks the predictions according to the over-representation with respect to a random background based on a Markov model.
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PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences.
Šulc M, Marín RM, Robins HS, Vaníček J.
Nucleic Acids Res. 2015 May 6. pii: gkv457
Searching the coding region for microRNA targets.
Marín RM, Sulc M, Vanícek J.
RNA. 2013 Apr;19(4):467-74. doi: 10.1261/rna.035634.112.
Optimal use of conservation and accessibility filters in microRNA target prediction.
Marín RM, Vanícek J.
PLoS One. 2012;7(2):e32208. doi: 10.1371/journal.pone.0032208.