From 7c907e07050bc77a2ecbca41c5237a065587ab6f Mon Sep 17 00:00:00 2001 From: Daniel Barton Date: Fri, 30 Aug 2013 17:35:00 +0100 Subject: [PATCH] A secondary parameters file with some Jalview friendly parameters --- testsrc/testdata/RNAalifoldParameters.xml | 134 +++++++++++++++++++++++++++++ 1 file changed, 134 insertions(+) create mode 100644 testsrc/testdata/RNAalifoldParameters.xml diff --git a/testsrc/testdata/RNAalifoldParameters.xml b/testsrc/testdata/RNAalifoldParameters.xml new file mode 100644 index 0000000..7cae870 --- /dev/null +++ b/testsrc/testdata/RNAalifoldParameters.xml @@ -0,0 +1,134 @@ + + + + compbio.runner.structure.RNAalifold + + Endgaps + Score pairs with endgaps same as gap-gap pairs + -E + + + Most Informative Sequence + Ouput Set of nucleotides with frequency > average + --mis + + + Partition Function + Output partition function and probability matrix + -p + + + Circular + Assume circular RNA molecule + -c + + + + G-Quadruplex + Incorporate G-Quadruplex formation into prediction algorithm + -g + + + d2 + dangling energies will be added for the bases adjacent to a helix on both sides + -d2 + + + No LP + Produce Structures without lonely pairs + --noLP + + + No GU + Do not allow GU pairs + --noGU + + + No Closing GU + Do not allow GU pairs at the end of sequences + --noClosingGU + + + old + Use old energy evaluation, treating gaps as characters + --old + + + Ribosum Scoring + Use Ribosum Scoring Matrix + -r + + + d2 + + Dangling energies are added for the bases adjacent to a helix on both sides + + -d2 + + + MEA Structure + Maximum Expected Accuracy Structure + --MEA + + + + + + scaling factor + In calculating pf use scale*mfe as estimate for ensemble free energy] + -S + 1.07 + + Float + 0 + 100 + + + + bppmThreshold + Threshold for base pair probabilities + --bppmThreshold + 0.000001 + + Float + 0.0000000000001 + 1.0 + + + + Temperature + Rescale Energy parameterss to Temperature + -T + 37 + + Float + -274 + 1000000 + + + + + cfactor + weight of covariance term + --cfactor + 1.0 + + Float + 0 + 100000 + + + + nfactor + penalty for non-compatible sequences in covariance term + --nfactor + 1.0 + + Float + 0 + 100000 + + + + \ No newline at end of file -- 1.7.10.2