Error: Invalid request
fit.final.json
generated by the compute server (see above), our software package ProBoundTools can be used to predict the relative affinities of new sequences. This utility was developed in Java (downloaded here) and is verified for version 1.8.0_91. A tarball containing the JAR file with all dependencies can be downloaded here (the underlying source code is also accessable on GitHub).tar -xvf ProBoundTools.tar.gz
export PROBOUND_DIR="/path/to/ProBoundTools"
alias proBoundTools='java -cp $PROBOUND_DIR/ProBoundTools/target/ProBound-jar-with-dependencies.jar proBoundTools/App'
Here /path/to/ProBoundTools
should be replaced with the directory created by tar
.
AAAAGACGACTGCGGTCACTGAGGTGTAAA
ACTGTTTGCTCTATGCGGAGGAGCCCCTTA
TTAACTGGGTATAGGGGCGAATATGGCGAC
TTAGCCGGGAGGGGGCGCTCCGTAGTGGAT
ATAGTAGTCGTGCGCCCCCACTGGTGACAA
TGTTCCTTGCTTTTATAAGGTAAATGCAGG
(stored in the file seq.txt
), the total relative affinity for each sequence is computed using the terminal commandproBoundTools -c 'loadFitLine(fit.final.json).buildConsensusModel().addNScoring().selectBindingMode(1).inputTXT(seq.txt).bindingModeScores(/dev/stdout)'
AAAAGACGACTGCGGTCACTGAGGTGTAAA 3.06461e-05
ACTGTTTGCTCTATGCGGAGGAGCCCCTTA 1.00708e-04
TTAACTGGGTATAGGGGCGAATATGGCGAC 5.30426e-05
TTAGCCGGGAGGGGGCGCTCCGTAGTGGAT 7.04016e-02
ATAGTAGTCGTGCGCCCCCACTGGTGACAA 1.58707e-03
TGTTCCTTGCTTTTATAAGGTAAATGCAGG 2.71934e-06
Here
loadFitLine(fit.final.json)
: Loads the ProBound fit.buildConsensusModel()
: Reconciles experiment- and round-specifc activities and adjusts the position-specific affinity matrix (PSAM) so that the maximum relative affinity for each binding offset is 1.0 (use writeModel(/dev/stdout)
to inspect the updated model).addNScoring()
: Extends the alphabet to support the wildcard character 'N'.selectBindingMode(1)
: Selects the second (zero indexed) binding mode (PSAM).inputTXT(seq.txt)
: Specifies where the input sequences are located. All sequences must be of equal length.bindingModeScores(/dev/stdout)
: Computes the relative affinity for each offset/strand and reports the sum to standard output. The affinities for each offset/strand can instead be reported using bindingModeScores(/dev/stdout,profile)
.
java -cp ProBoundTools.jar proBoundTools/App -help
loadMotifCentralModel(modelID)
(instead of loadFitLine(fit.final.json)
).