资 源 简 介
SABINE is a tool to predict the binding specificity of a transcription factor (TF), given its amino acid sequence, DNA-binding domains, superclass and species. The tool compares a given factor to a predefined set of TFs of the same superclass for which experimentally confirmed position frequency matrices (PFM) are available. Based on various features capturing evolutionary, structural and physicochemical similarity of the DNA-binding domains, the PFM similarity is predicted by means of support vector regression. The TFs with highest PFM similarity to the factor of interest are reported and their PFMs are merged using STAMP to generate the predicted consensus PFM.
文 件 列 表
biojava-1.5.jar
core
SequenceAligner.class
IrrelevantPairIdentifier.class
SequenceFeatureCalculator.class
IrrelevantPairIdentifier.java
DomainFeatureCalculator.class
SpeciesFeatureCalculator.class
SVMPairwiseFeatureCalculator.java
SequenceFeatureCalculator.java
FeatureRepairer.class
SpeciesFeatureCalculator.java
SVMPairwiseFeatureCalculator.class
DomainFeatureCalculator.java
FeatureRepairer.java
SequenceAligner.java
extension
ProdoricParser.java
OutfileGenerator.class
DBDEnsemblParser.class
UniprotParser.java
RegTransBaseParser.java
PFMFormatConverter.java
DPInteractParser.class
InfileSplitter.java
ProdoricParser.class
TrainingsetParser.java
DatabaseParser.class
SABINEInputOutputParser.java
RegulonDBParser.java
TransfacParser.java
PWMModelFileParser.java
SABINEInputfileWriter.class
SABINEInputfileWriter.java
OutfileScanner.java
SABINETrainingsetParser.java
PWMModelFileParser.class
PWMSimilarityCalculator.class
PFMFormatConverter.class
PredictionEvaluator.java
SABINEParser.java
UniProtParser4Procaryotes.class
PWMSimilarityCalculator.java
DatabaseParser.java
DBDEnsemblParser.java
SwissRegulonParser.java
SpeciesMappingParser.class
IDMappingParser.class
OutfileGenerator.java
PredictionEvaluator.class
DirectoryRemover.java
UniprotParser.class
DBDParser.class
SABINEParser.class
SABINETrainingsetParser.class
InfileSplitter.class
OutfileScanner.class
SwissRegulonParser.class
InterproParser.java
SpeciesMappingParser.java
RegTransBaseParser.class
TrainingsetParser.class
InterproParser.class
UniProtParser4Procaryotes.java
OutfileWriter.class
SABINEInputOutputParser.class
IDMappingParser.java
DPInteractParser.java
RegulonDBParser.class
MatrixFileParser.java
MatrixFileParser.class
DBDParser.java
OutfileWriter.java
TransfacParser.class
FBPPredictor.class
FBPPredictor.java
GSL
gsl-1.10.tar.gz
gui
JHelpBrowser.java
SystemBrowser.java
JBrowser.java
SABINEfileFilter.java
LayoutHelper.java
MessageListener.java
SequenceLogo.java
MessageProcessor.java
help
SequenceAligner.class
FileFilter.class
RawDataPreprocessor.class
FileFilter$FormatFileFilter.class
LibSVMFeatureScaler.class
FileCopier.java
FeatureFileGenerator.class
ModelFileObtainer.java
RawDataPreprocessor.java
TFNamePairsFileGenerator.class
LibSVMFeatureScaler.java
RandomStringGenerator.java
TimeStampGenerator.java
ModelFileObtainer.class
LibSVMFileGenerator.java
LibSVMFileGenerator.class
FormatConverter.class
DomainMatrixSequenceExtractor.class
TFNamePairsFileGenerator.java
RandomStringGenerator.class
FileFilter.java
DomainMatrixSequenceExtractor.java
FormatConverter.java
FeatureFileGenerator.java
SequenceAligner.java
input
test.tf
install.sh
internal
22.12.2009_14:18
30.11.2009_15:33
25.09.2009_18:03
basedir2
22.12.2009_14:33
25.09.2009_18:10
sample_neg.labels
13.07.2009_11:54
basedir1
sample_neg.input
30.11.2009_14:53
sample_pos.labels
30.11.2009_15:08
basedir3
sample_pos.input
prediction.out
12.07.2009_18:35
22.12.2009_14:34
30.11.2009_14:33
infile.tmp
libsvmfiles
my_basedir
30.11.2009_15:32
relevantpairs
allpairs
sample_pos.output
30.11.2009_14:34
sample_neg.output
30.11.2009_14:55
30.11.2009_15:37
02.10.2009_15:52
30.11.2009_14:37
30.11.2009_15:34
30.11.2009_14:36
30.11.2009_14:54
jmathplot.jar
LAKernel
LAkernel_all_vs_all
LAkernel_1_vs_all.o
seqio.o
LAkernel.h
readme
test_script.sh
pam250.dat
LAkernel_all_vs_all.o
LAkernel_1_vs_all
JTTopt.dat
LAkernel.c
LAkernel_all_vs_all.c
Makefile.def
LAkernel_direct.o
blosum62.dat
LAkernel_direct.c
PAM_250opt.dat
seqio.h
Makefile
LAkernel.o
seqio.c
Makefile~
LAkernel_MPI.c
GCBopt.dat
LAkernel_direct
protein.dat
Makefile.mpi_intel
BLOSUM_62opt.dat
parameters.dat
Makefile.mpi_sgi
LAkernel_1_vs_all.c
libsvm
STAMPRunner.class
AppletFrame$1.class
svm_toy$4.class
svm_toy.java
AppletFrame.class
svm_predict.java
STAMPRunner.java
svm_train.class
svm_toy$2.class
SVMPredictor.class
svm_toy$6.class
svm_toy$3.class
svm_toy.class
svm_train.java
svm_toy$1.class
PWMOutlierFilter.java
LabeledTF.class
LabeledTF.java
svm_toy$5.class
PWMOutlierFilter.class
svm_predict.class
svm_toy$point.class
SVMPredictor.java
libsvmcore
svm$decision_function.class
svm_problem.class
svm_model.class
ONE_CLASS_Q.class
SVR_Q.class
svm.class
Solver.class
Kernel.class
svm.java
Solver$SolutionInfo.class
Cache.class
QMatrix.class
Cache$head_t.class
svm_model.java
svm_problem.java
svm_node.class
Solver_NU.class
svm_parameter.java
svm_node.java
svm_parameter.class
SVC_Q.class
license.txt
MismatchKernel
src
perl
data
matrix
model
FeatureSelector.java
SingleFeatureEvaluator.java
SingleFeatureEvaluator.class
LabelFileGenerator.java
ModelGenerator.class
FeatureSelector.class
ModelGenerator.java
LabelFileGenerator.class
models
class3
class4
class2
class0
class1
MoSta
code
optimization
MatrixConverter.java
MatrixConverter.class
MatlignOptimizer.class
MoStaOptimizer.java
MoStaOptimizer.class
MatlignOptimizer.java
Optimizer.class
Optimizer.java
plot
PlotGenerator.java
PlotGenerator.class
PSIPRED
.ss
launchPSIPRED
readme
launchPSIPRED~
seq.horiz
src
seq.ss2
seq.fasta~
--help.horiz
psitmp17715028617ac.mtx
.horiz
runpsipred_single
data
bin
runpsipred
dsxrbynjlx.horiz
-help.horiz
ximvqlcwee.horiz
psitmp29460286adad.mtx
license
seq.ss
backup
psitmp136680286adad.mtx
seq.fasta
readme.txt
readme.txt~
resources
Resource.java
Resource.class
img
html
txt
SABINE_Caller.class
SABINE_Caller.java
sabine.jar
sabine.sh
STAMP
outfile_matched.transfac
input.motifs
launchSTAMP
test.motifs~
output.tree
output_matched.transfac
ScoreDists
outfile_match_pairs.txt
sample.motifs
launchSTAMP~
outfileFBP.txt
launchSTAMPWithParams
outfile.tree
install.txt
output_match_pairs.txt
jaspar.motifs
input.motifs~
license.txt
test.motifs
code
launchSTAMP_old
substitutionMatrices
MUET020101.dat
VOGG950101.dat
BENS940103.dat
RUSR970101.dat
DAYM780301.dat
NGPC000101.dat
KANM000101.dat
PRLA000102.dat
DOSZ010103.dat
LUTR910101.dat
blosum_n.dat
RIER950101.dat
MIYT790101.dat
MIYS930101.dat
GEOD900101.dat
NIEK910101.dat
WEIL970101.dat
QU_C930102.dat
KOLA920101.dat
GRAR740104.dat
PRLA000101.dat
LUTR910106.dat
JOND940101.dat
dayhoff.dat
AZAE970101.dat
MEHP950103.dat
MEHP950101.dat
QU_C930101.dat
SS-matrix.dat
pam_250.dat
MEHP950102.dat
AZAE970102.dat
LUTR910103.dat
RUSR970103.dat
BLOSUM_50.dat
DOSZ010101.dat
GIAG010101.dat
pam_150.dat
TUDE900101.dat
DOSZ010102.dat
QU_C930103.dat
BENS940101.dat
OVEJ920101.dat
QUIB020101.dat
ALTS910101.dat
CROG050101.dat
BENS940104.dat
RUSR970102.dat
BLOSUM_90.dat
pam_030.dat
LUTR910108.dat
JOHM930101.dat
JOND920103.dat
CSEM940101.dat
PAM_010.dat
pam_100.dat
RISJ880101.dat
BLOSUM_30.dat
BLOSUM_40.dat
HENS920101.dat
BLOSUM_62.dat
NAOD960101.dat
MOHR870101.dat
BLOSUM_80.dat
DAYM780302.dat
BLOSUM_70.dat
LUTR910107.dat
HENS920104.dat
HENS920103.dat
GONG920101.dat
LUTR910109.dat
MCLA720101.dat
BENS940102.dat
FITW660101.dat
LUTR910102.dat
BLAJ010101.dat
MCLA710101.dat
LEVJ860101.dat
PAM_080.dat
pam_400.dat
MUET020102.dat
MUET010101.dat
FEND850101.dat
WEIL970102.dat
LUTR910105.dat
OGAK980101.dat
KAPO950101.dat
pam_050.dat
pam_130.dat
NIEK910102.dat
LUTR910104.dat
HENS920102.dat
pam_500.dat
DOSZ010104.dat
tmp
trainingsets_public
FBPs_class0.out
temp_class4
trainingset_class2.fbps
feature_scaling_orientation_class1.out
FBPs_class2.out
trainingset_all_classes.fbps
class4.30featurenames
feature_scaling_orientation_class2.out
trainingset_class4.tfnames
trainingset_class4.rawdata
feature_scaling_orientation_class3.out
domain_scores_PAM_080_class4.out
trainingset_class2.species
domain_scores_BLOSUM_62_class4.out
trainingset_class3.species
trainingset_class1.rawdata
domain_scores_PAM_080_class3.out
trainingset_class4.blo62
class1.30featurenames
feature_scaling_orientation_class0.out
trainingset_class3.fbps
sequences_matrices_class2.out
trainingset_class4.fbps
trainingset_class0.blo62
domain_scores_BLOSUM_62_class0.out
trainingset_class0.tfnames
trainingset_class1.fbps
trainingset_class1.blo62
class2.30featurenames
trainingset_class0.secstruct
domain_scores_PAM_080_class0.out
Classes
trainingset_class3.tfnames
trainingset_class1.tfnames
sequences_matrices_class4.out
domain_scores_BLOSUM_62_class2.out
new_phylogenetic_distances.out
domain_scores_BLOSUM_62_class1.out
trainingset_public.txt
trainingset_class3.blo62
trainingset_class1.pam80
FBPs_class1.out
trainingset_class4.secstruct
sequences_matrices_class3.out
sequences_matrices_class1.out
trainingset_class3.rawdata
trainingset_class2.tfnames
sequences_matrices_class0.out
class0.30featurenames
trainingset_class0.rawdata
domain_scores_BLOSUM_62_class3.out
trainingset_class1.species
trainingset_class3.pam80
trainingset_class1.secstruct
trainingset_class2.rawdata
trainingset_class2.secstruct
feature_scaling_orientation_class4.out
trainingset_class3.secstruct
domain_scores_PAM_080_class2.out
temp_class3
trainingset_class2.blo62
trainingset_class4.species
trainingset_class0.species
trainingset_class0.fbps
class3.30featurenames
temp_class1
trainingset_class4.pam80
trainingset_class2.pam80
FBPs_class3.out
FBPs_class4.out
trainingset_class0.pam80
temp_class2
temp_class0
domain_scores_PAM_080_class1.out
