Words similar to mfold

Example sentences for: mfold

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We analyzed conserved regions with mfold 3.1, an RNA-folding algorithm [ 41 ] . As miRNA genes can be located on either strand, and the quality of predicted hairpin structures can vary significantly between the respective strands (depending on the amount of G-U base-pairing), we folded each region as both the forward and the reverse complement of the extracted sequence (436,000 regions × 2 = 872,000 mfolds).
All Dm regions were folded with mfold 3.1 by submitting parallel batches of 500 mfolds to the cluster nodes and copying the .det and .out mfold output files to a final storage destination.
Given a 100-nucleotide input sequence, mfold 3.1 typically returns one to six alternate structures, each containing one to four helical arms; thus, the structure containing the highest-scoring helical arm had to be determined for each folded sequence.
The mfold computer program version 3.0 http://bioinfo.math.rpi.edu/~mfold/rna/form1.cgiwas used to predict the RNA secondary structure and to calculate the folding free energy [ 26 27 ] . We have computed the minimum-free-energy structures from all the donor- and acceptor sites of the 60 exons of NF1 within a window of 100 bp.
Since mfold tends to insert small helices within terminal loops that falsely reduce the size of the terminal loop, small terminal loops (3, 4 or 5 nucleotides in length) were extended to seven nucleotides.