May 132015
 

PACCMIT-CDS / PACCMIT

:: DESCRIPTION

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.

::DEVELOPER

LABORATORY OF THEORETICAL PHYSICAL CHEMISTRY, LCPT

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PACCMIT-CDS

:: MORE INFORMATION

Citation

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.

78 views

Sorry, the comment form is closed at this time.