perl np_parse_ProteinProphet.pl yeast_example_MSMS_LTQOrbiTrap_8inj-prot.xml 0.05 yeast_TRAINING

perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES.arf yeast_TRAINING_0.05.protlst yeast 1 100 0 0 N
perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES.arf yeast_TRAINING_0.05.protlst yeast 1 200 0 0 N
perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES.arf yeast_TRAINING_0.05.protlst yeast 1 300 0 0 N 
perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES.arf yeast_TRAINING_0.05.protlst yeast 1 0 1 10 N
perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES.arf yeast_TRAINING_0.05.protlst yeast 1 0 1 30 N 

perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES_AAonly.arf yeast_TRAINING_0.05.protlst yeast_AAonly 1 200 0 0 N
perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES_Lengthonly.arf yeast_TRAINING_0.05.protlst yeast_Lengthonly 1 200 0 0 N


#####


Other_Training_Sets

	other .arff for different parameter settings (see above)

Results_AttributeSelect

	resultbuffers for attribute selection runs

Results_Training

	saved resultbuffers from WEKA training runs

yeast_66attrib.select.gz
yeast_66attrib_TRAINING_prprob1_prspec200_peprob0_pespec0_10xCV.result.gz

	resultbuffer for final model

yeast_66attrib_TRAINING_prprob1_prspec200_peprob0_pespec0.arff.gz
yeast_66attrib_TRAINING_prprob1_prspec200_peprob0_pespec0.log.gz

	data for final model

yeast_attrib66_p1p200p0p0.model.gz

	final model

yeast_example_MSMS_LTQOrbiTrap_8inj-prot.xml.gz
yeast_TRAINING_0.05.protlst.gz

	original MS/MS data for training	

yeast_PEPTIDE_PROPERTIES_66attrib.arf.gz
yeast_PEPTIDE_PROPERTIES_AAonly.arf.gz
yeast_PEPTIDE_PROPERTIES.arf.gz
yeast_PEPTIDE_PROPERTIES_Lengthonly.arf.gz
yeast_PEPTIDE_PROPERTIES_relAAonly.arf.gz

	all yeast proteins (and their peptides' attributes -- different types and numbers of attributes)


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