# HG changeset patch # User tyty # Date 1427144053 14400 # Node ID 59862169c998b081493f2b1f5a54ff2dee64873a # Parent 976d4a6625a5c689e62efcf3c4f7d457a21dc014 Uploaded diff -r 976d4a6625a5 -r 59862169c998 predict/predict_RNAs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/predict/predict_RNAs.xml Mon Mar 23 16:54:13 2015 -0400 @@ -0,0 +1,124 @@ + + predict RNA structures with or without experimental constraints from the Reactivity Calculation module + + #if $program.wh == "rs" + #if $program.rs_reactivity.type == "restraint" + predict_RNAs.py $rna_list $reference_file $program.rs_reactivity.type $temperature $program.wh $output $program.rs_reactivity.reactivity_file $program.rs_reactivity.slope $program.rs_reactivity.intercept + #else + predict_RNAs.py $rna_list $reference_file $program.rs_reactivity.type $temperature $program.wh $output + #end if + #else + #if $program.vp_reactivity.type == "restraint" + predict_RNAs.py $rna_list $reference_file $program.vp_reactivity.type $temperature $program.wh $output $program.vp_reactivity.reactivity_file $program.vp_reactivity.threshold_high $program.vp_reactivity.threshold_low $program.gqs + #else + predict_RNAs.py $rna_list $reference_file $program.vp_reactivity.type $temperature $program.wh $output $program.gqs + #end if + #end if + + + + + + + + + biopython + numpy + matplotlib + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**Function** + +RNA Structure Prediction uses the RNAstructure program (V5.6) and ViennaRNA package (V2.1.9) to predict RNA structures without restraints (in silico) or with restraints from structural reactivities, as provided by the Reactivity Calculation module. Users can designate the temperature under which to predict the RNA structures. + +----- + +**Input**: + +* 1. A file with transcript Ids (Max num. 100), (each ID one line) +* 2. Reference file (fasta) used to map the reads to +* 3. Temperature for RNA structure prediction +* [Optional]: +* 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided +* /RNAstructure prediction mode/ +* 2. Slope used with structural restraints (default 1.8) +* 3. Intercept used with structural restraints (default -0.6) +* /ViennaRNA package prediction mode/ +* 2. Flag that determines whether to incoorporate G-Quadruplex prediction +* 3. High reactivity threshold (Any nucleotide with structural reactivity that is higher than it will be constrainted as single stranded) (default 0.6) +* 4. Low reactivity threshold (Any nucleotide with structural reactivity that is lower than it will be constrainted as double stranded) (default 0.3) + +----- + +**Output**: + +* 1. Dot bracket files with predicted RNA structures [transciptID.dbn] +* 2. .ps files which depict the predicted RNA structures [transciptID.ps] +* [Optional] +* 3. .png files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.png] + +----- + +**Attention** + +Make sure that none of the transcript Ids contains a "|" or a space! + +----- + +**Backend program**: + +* 1. This module uses RNAstructure (http://rna.urmc.rochester.edu/RNAstructure.html) or ViennaRNA package (http://www.tbi.univie.ac.at/RNA/) as the backend programs to predict RNA structures. +* 2. Default parameters are used for RNAstructure and ViennaRNA package except -T (Temperature), -sm (slope used with SHAPE restraints [RNAstructure prediction mode]), -si (intercept used with SHAPE restraints [RNAstructure prediction mode]) and thresholds for high and low reactivity [ViennaRNA package prediciton mode], for which users can specify the value + + + + +