mspire 0.4.9 → 0.5.0
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- data/README +27 -17
- data/changelog.txt +31 -62
- data/lib/ms/calc.rb +32 -0
- data/lib/ms/data/interleaved.rb +60 -0
- data/lib/ms/data/lazy_io.rb +73 -0
- data/lib/ms/data/lazy_string.rb +15 -0
- data/lib/ms/data/simple.rb +59 -0
- data/lib/ms/data/transposed.rb +41 -0
- data/lib/ms/data.rb +57 -0
- data/lib/ms/format/format_error.rb +12 -0
- data/lib/ms/spectrum.rb +25 -384
- data/lib/ms/support/binary_search.rb +126 -0
- data/lib/ms.rb +10 -10
- metadata +38 -350
- data/INSTALL +0 -58
- data/README.rdoc +0 -18
- data/Rakefile +0 -330
- data/bin/aafreqs.rb +0 -23
- data/bin/bioworks2excel.rb +0 -14
- data/bin/bioworks_to_pepxml.rb +0 -148
- data/bin/bioworks_to_pepxml_gui.rb +0 -225
- data/bin/fasta_shaker.rb +0 -5
- data/bin/filter_and_validate.rb +0 -5
- data/bin/gi2annot.rb +0 -14
- data/bin/id_class_anal.rb +0 -112
- data/bin/id_precision.rb +0 -172
- data/bin/ms_to_lmat.rb +0 -67
- data/bin/pepproph_filter.rb +0 -16
- data/bin/prob_validate.rb +0 -6
- data/bin/protein_summary.rb +0 -6
- data/bin/protxml2prots_peps.rb +0 -32
- data/bin/raw_to_mzXML.rb +0 -55
- data/bin/run_percolator.rb +0 -122
- data/bin/sqt_group.rb +0 -26
- data/bin/srf_group.rb +0 -27
- data/bin/srf_to_sqt.rb +0 -40
- data/lib/align/chams.rb +0 -78
- data/lib/align.rb +0 -154
- data/lib/archive/targz.rb +0 -94
- data/lib/bsearch.rb +0 -120
- data/lib/core_extensions.rb +0 -16
- data/lib/fasta.rb +0 -626
- data/lib/gi.rb +0 -124
- data/lib/group_by.rb +0 -10
- data/lib/index_by.rb +0 -11
- data/lib/merge_deep.rb +0 -21
- data/lib/ms/converter/mzxml.rb +0 -77
- data/lib/ms/gradient_program.rb +0 -170
- data/lib/ms/msrun.rb +0 -244
- data/lib/ms/msrun_index.rb +0 -108
- data/lib/ms/parser/mzdata/axml.rb +0 -67
- data/lib/ms/parser/mzdata/dom.rb +0 -175
- data/lib/ms/parser/mzdata/libxml.rb +0 -7
- data/lib/ms/parser/mzdata.rb +0 -31
- data/lib/ms/parser/mzxml/axml.rb +0 -70
- data/lib/ms/parser/mzxml/dom.rb +0 -182
- data/lib/ms/parser/mzxml/hpricot.rb +0 -253
- data/lib/ms/parser/mzxml/libxml.rb +0 -19
- data/lib/ms/parser/mzxml/regexp.rb +0 -122
- data/lib/ms/parser/mzxml/rexml.rb +0 -72
- data/lib/ms/parser/mzxml/xmlparser.rb +0 -248
- data/lib/ms/parser/mzxml.rb +0 -282
- data/lib/ms/parser.rb +0 -108
- data/lib/ms/precursor.rb +0 -25
- data/lib/ms/scan.rb +0 -81
- data/lib/mspire.rb +0 -4
- data/lib/pi_zero.rb +0 -244
- data/lib/qvalue.rb +0 -161
- data/lib/roc.rb +0 -187
- data/lib/sample_enzyme.rb +0 -160
- data/lib/scan_i.rb +0 -21
- data/lib/spec_id/aa_freqs.rb +0 -170
- data/lib/spec_id/bioworks.rb +0 -497
- data/lib/spec_id/digestor.rb +0 -138
- data/lib/spec_id/mass.rb +0 -179
- data/lib/spec_id/parser/proph.rb +0 -335
- data/lib/spec_id/precision/filter/cmdline.rb +0 -218
- data/lib/spec_id/precision/filter/interactive.rb +0 -134
- data/lib/spec_id/precision/filter/output.rb +0 -148
- data/lib/spec_id/precision/filter.rb +0 -637
- data/lib/spec_id/precision/output.rb +0 -60
- data/lib/spec_id/precision/prob/cmdline.rb +0 -160
- data/lib/spec_id/precision/prob/output.rb +0 -94
- data/lib/spec_id/precision/prob.rb +0 -249
- data/lib/spec_id/proph/pep_summary.rb +0 -104
- data/lib/spec_id/proph/prot_summary.rb +0 -484
- data/lib/spec_id/proph.rb +0 -4
- data/lib/spec_id/protein_summary.rb +0 -489
- data/lib/spec_id/sequest/params.rb +0 -316
- data/lib/spec_id/sequest/pepxml.rb +0 -1458
- data/lib/spec_id/sequest.rb +0 -33
- data/lib/spec_id/sqt.rb +0 -349
- data/lib/spec_id/srf.rb +0 -973
- data/lib/spec_id.rb +0 -778
- data/lib/spec_id_xml.rb +0 -99
- data/lib/transmem/phobius.rb +0 -147
- data/lib/transmem/toppred.rb +0 -368
- data/lib/transmem.rb +0 -157
- data/lib/validator/aa.rb +0 -48
- data/lib/validator/aa_est.rb +0 -112
- data/lib/validator/background.rb +0 -77
- data/lib/validator/bias.rb +0 -95
- data/lib/validator/cmdline.rb +0 -431
- data/lib/validator/decoy.rb +0 -107
- data/lib/validator/digestion_based.rb +0 -70
- data/lib/validator/probability.rb +0 -51
- data/lib/validator/prot_from_pep.rb +0 -234
- data/lib/validator/q_value.rb +0 -32
- data/lib/validator/transmem.rb +0 -272
- data/lib/validator/true_pos.rb +0 -46
- data/lib/validator.rb +0 -197
- data/lib/xml.rb +0 -38
- data/lib/xml_style_parser.rb +0 -119
- data/lib/xmlparser_wrapper.rb +0 -19
- data/release_notes.txt +0 -2
- data/script/compile_and_plot_smriti_final.rb +0 -97
- data/script/create_little_pepxml.rb +0 -61
- data/script/degenerate_peptides.rb +0 -47
- data/script/estimate_fpr_by_cysteine.rb +0 -226
- data/script/extract_gradient_programs.rb +0 -56
- data/script/find_cysteine_background.rb +0 -137
- data/script/genuine_tps_and_probs.rb +0 -136
- data/script/get_apex_values_rexml.rb +0 -44
- data/script/histogram_probs.rb +0 -61
- data/script/mascot_fix_pepxml.rb +0 -123
- data/script/msvis.rb +0 -42
- data/script/mzXML2timeIndex.rb +0 -25
- data/script/peps_per_bin.rb +0 -67
- data/script/prep_dir.rb +0 -121
- data/script/simple_protein_digestion.rb +0 -27
- data/script/smriti_final_analysis.rb +0 -103
- data/script/sqt_to_meta.rb +0 -24
- data/script/top_hit_per_scan.rb +0 -67
- data/script/toppred_to_yaml.rb +0 -47
- data/script/tpp_installer.rb +0 -249
- data/specs/align_spec.rb +0 -79
- data/specs/bin/bioworks_to_pepxml_spec.rb +0 -79
- data/specs/bin/fasta_shaker_spec.rb +0 -259
- data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +0 -199
- data/specs/bin/filter_and_validate_spec.rb +0 -180
- data/specs/bin/ms_to_lmat_spec.rb +0 -34
- data/specs/bin/prob_validate_spec.rb +0 -86
- data/specs/bin/protein_summary_spec.rb +0 -14
- data/specs/fasta_spec.rb +0 -354
- data/specs/gi_spec.rb +0 -22
- data/specs/load_bin_path.rb +0 -7
- data/specs/merge_deep_spec.rb +0 -13
- data/specs/ms/gradient_program_spec.rb +0 -77
- data/specs/ms/msrun_spec.rb +0 -498
- data/specs/ms/parser_spec.rb +0 -92
- data/specs/ms/spectrum_spec.rb +0 -87
- data/specs/pi_zero_spec.rb +0 -115
- data/specs/qvalue_spec.rb +0 -39
- data/specs/roc_spec.rb +0 -251
- data/specs/rspec_autotest.rb +0 -149
- data/specs/sample_enzyme_spec.rb +0 -126
- data/specs/spec_helper.rb +0 -135
- data/specs/spec_id/aa_freqs_spec.rb +0 -52
- data/specs/spec_id/bioworks_spec.rb +0 -148
- data/specs/spec_id/digestor_spec.rb +0 -75
- data/specs/spec_id/precision/filter/cmdline_spec.rb +0 -20
- data/specs/spec_id/precision/filter/output_spec.rb +0 -31
- data/specs/spec_id/precision/filter_spec.rb +0 -246
- data/specs/spec_id/precision/prob_spec.rb +0 -44
- data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
- data/specs/spec_id/proph/pep_summary_spec.rb +0 -98
- data/specs/spec_id/proph/prot_summary_spec.rb +0 -128
- data/specs/spec_id/protein_summary_spec.rb +0 -189
- data/specs/spec_id/sequest/params_spec.rb +0 -68
- data/specs/spec_id/sequest/pepxml_spec.rb +0 -374
- data/specs/spec_id/sequest_spec.rb +0 -38
- data/specs/spec_id/sqt_spec.rb +0 -246
- data/specs/spec_id/srf_spec.rb +0 -172
- data/specs/spec_id/srf_spec_helper.rb +0 -139
- data/specs/spec_id_helper.rb +0 -33
- data/specs/spec_id_spec.rb +0 -366
- data/specs/spec_id_xml_spec.rb +0 -33
- data/specs/transmem/phobius_spec.rb +0 -425
- data/specs/transmem/toppred_spec.rb +0 -298
- data/specs/transmem_spec.rb +0 -60
- data/specs/transmem_spec_shared.rb +0 -64
- data/specs/validator/aa_est_spec.rb +0 -66
- data/specs/validator/aa_spec.rb +0 -40
- data/specs/validator/background_spec.rb +0 -67
- data/specs/validator/bias_spec.rb +0 -122
- data/specs/validator/decoy_spec.rb +0 -51
- data/specs/validator/fasta_helper.rb +0 -26
- data/specs/validator/prot_from_pep_spec.rb +0 -141
- data/specs/validator/transmem_spec.rb +0 -146
- data/specs/validator/true_pos_spec.rb +0 -58
- data/specs/validator_helper.rb +0 -33
- data/specs/xml_spec.rb +0 -12
- data/test_files/000_pepxml18_small.xml +0 -206
- data/test_files/020a.mzXML.timeIndex +0 -4710
- data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +0 -3973
- data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +0 -3872
- data/test_files/4-03-03_small-prot.xml +0 -321
- data/test_files/4-03-03_small.xml +0 -3876
- data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
- data/test_files/bioworks-3.3_10prots.xml +0 -5999
- data/test_files/bioworks31.params +0 -77
- data/test_files/bioworks32.params +0 -62
- data/test_files/bioworks33.params +0 -63
- data/test_files/bioworks_single_run_small.xml +0 -7237
- data/test_files/bioworks_small.fasta +0 -212
- data/test_files/bioworks_small.params +0 -63
- data/test_files/bioworks_small.phobius +0 -109
- data/test_files/bioworks_small.toppred.out +0 -2847
- data/test_files/bioworks_small.xml +0 -5610
- data/test_files/bioworks_with_INV_small.xml +0 -3753
- data/test_files/bioworks_with_SHUFF_small.xml +0 -2503
- data/test_files/corrupted_900.srf +0 -0
- data/test_files/head_of_7MIX.srf +0 -0
- data/test_files/interact-opd1_mods_small-prot.xml +0 -304
- data/test_files/messups.fasta +0 -297
- data/test_files/opd1/000.my_answer.100lines.xml +0 -101
- data/test_files/opd1/000.tpp_1.2.3.first10.xml +0 -115
- data/test_files/opd1/000.tpp_2.9.2.first10.xml +0 -126
- data/test_files/opd1/000.v2.1.mzXML.timeIndex +0 -3748
- data/test_files/opd1/000_020-prot.png +0 -0
- data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +0 -62
- data/test_files/opd1/000_020_3prots-prot.xml +0 -62
- data/test_files/opd1/opd1_cat_inv_small-prot.xml +0 -139
- data/test_files/opd1/sequest.3.1.params +0 -77
- data/test_files/opd1/sequest.3.2.params +0 -62
- data/test_files/opd1/twenty_scans.mzXML +0 -418
- data/test_files/opd1/twenty_scans.v2.1.mzXML +0 -382
- data/test_files/opd1/twenty_scans_answ.lmat +0 -0
- data/test_files/opd1/twenty_scans_answ.lmata +0 -9
- data/test_files/opd1_020_beginning.RAW +0 -0
- data/test_files/opd1_2runs_2mods/data/020.mzData.xml +0 -683
- data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +0 -382
- data/test_files/opd1_2runs_2mods/data/040.mzData.xml +0 -683
- data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +0 -382
- data/test_files/opd1_2runs_2mods/data/README.txt +0 -6
- data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +0 -753
- data/test_files/orbitrap_mzData/000_cut.xml +0 -1920
- data/test_files/pepproph_small.xml +0 -4691
- data/test_files/phobius.small.noheader.txt +0 -50
- data/test_files/phobius.small.small.txt +0 -53
- data/test_files/s01_anC1_ld020mM.key.txt +0 -25
- data/test_files/s01_anC1_ld020mM.meth +0 -0
- data/test_files/small.fasta +0 -297
- data/test_files/small.sqt +0 -87
- data/test_files/smallraw.RAW +0 -0
- data/test_files/tf_bioworks2excel.bioXML +0 -14340
- data/test_files/tf_bioworks2excel.txt.actual +0 -1035
- data/test_files/toppred.small.out +0 -416
- data/test_files/toppred.xml.out +0 -318
- data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +0 -7
- data/test_files/validator_hits_separate/bioworks_small_HS.xml +0 -5651
- data/test_files/yeast_gly_small-prot.xml +0 -265
- data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +0 -6
- data/test_files/yeast_gly_small.xml +0 -3807
- data/test_files/yeast_gly_small2.parentTimes +0 -6
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Algorithm specific parameters:
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Full window size : 21
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Core window size : 11
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Wedge window size: 5
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Using hydrophobicity file: GES-scale
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Cutoff for certain transmembrane segments: 1.00
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9
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Cutoff for putative transmembrane segments: 0.60
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Critical distance between 2 transmembrane segments: 2
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11
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Critical loop length: 60
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Kingdom: eucaryote
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Using cyt/ext file: CYTEXT-scale
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Sequence : YAL001C (1160 res)
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MVLTIYPDELVQIVSDKIASNKGKITLNQLWDISGKYFDLSDKKVKQFVLSCVILKKDIE
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21
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VYCDGAITTKNVTDIIGDANHSYSVGITEDSLWTLLTGYTKKESTIGNSAFELLLEVAKS
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22
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GEKGINTMDLAQVTGQDPRSVTGRIKKINHLLTSSQLIYKGHVVKQLKLKKFSHDGVDSN
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23
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PYINIRDHLATIVEVVKRSKNGIRQIIDLKRELKFDKEKRLSKAFIAAIAWLDEKEYLKK
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24
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VLVVSPKNPAIKIRCVKYVKDIPDSKGSPSFEYDSNSADEDSVSDSKAAFEDEDLVEGLD
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25
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NFNATDLLQNQGLVMEEKEDAVKNEVLLNRFYPLQNQTYDIADKSGLKGISTMDVVNRIT
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26
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GKEFQRAFTKSSEYYLESVDKQKENTGGYRLFRIYDFEGKKKFFRLFTAQNFQKLTNAED
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27
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EISVPKGFDELGKSRTDLKTLNEDNFVALNNTVRFTTDSDGQDIFFWHGELKIPPNSKKT
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28
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PNKNKRKRQVKNSTNASVAGNISNPKRIKLEQHVSTAQEPKSAEDSPSSNGGTVVKGKVV
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29
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NFGGFSARSLRSLQRQRAILKVMNTIGGVAYLREQFYESVSKYMGSTTTLDKKTVRGDVD
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30
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LMVESEKLGARTEPVSGRKIIFLPTVGEDAIQRYILKEKDSKKATFTDVIHDTEIYFFDQ
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31
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TEKNRFHRGKKSVERIRKFQNRQKNAKIKASDDAISKKSTSVNVSDGKIKRRDKKVSAGR
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32
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TTVVVENTKEDKTVYHAGTKDGVQALIRAVVVTKSIKNEIMWDKITKLFPNNSLDNLKKK
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33
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WTARRVRMGHSGWRAYVDKWKKMLVLAIKSEKISLRDVEELDLIKLLDIWTSFDEKEIKR
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PLFLYKNYEENRKKFTLVRDDTLTHSGNDLAMSSMIQREISSLKKTYTRKISASTKDLSK
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35
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SQSDDYIRTVIRSILIESPSTTRNEIEALKNVGNESIDNVIMDMAKEKQIYLHGSKLECT
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36
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DTLPDILENRGNYKDFGVAFQYRCKVNELLEAGNAIVINQEPSDISSWVLIDLISGELLN
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37
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MDVIPMVRNVRPLTYTSRRFEIRTLTPPLIIYANSQTKLNTARKSAVKVPLGKPFSRLWV
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38
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NGSGSIRPNIWKQVVTMVVNEIIFHPGITLSRLQSRCREVLSLHEISEICKWLLERQVLI
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39
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TTDFDGYWVNHNWYSIYEST
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40
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41
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Found: 0 segments
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43
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44
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Sequence : YAL002W (1274 res)
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45
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MEQNGLDHDSRSSIDTTINDTQKTFLEFRSYTQLSEKLASSSSYTAPPLNEDGPKGVASA
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46
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VSQGSESVVSWTTLTHVYSILGAYGGPTCLYPTATYFLMGTSKGCVLIFNYNEHLQTILV
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47
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PTLSEDPSIHSIRSPVKSIVICSDGTHVAASYETGNICIWNLNVGYRVKPTSEPTNGMTP
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48
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TPALPAVLHIDDHVNKEITGLDFFGARHTALIVSDRTGKVSLYNGYRRGFWQLVYNSKKI
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49
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LDVNSSKEKLIRSKLSPLISREKISTNLLSVLTTTHFALILLSPHVSLMFQETVEPSVQN
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50
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SLVVNSSISWTQNCSRVAYSVNNKISVISISSSDFNVQSASHSPEFAESILSIQWIDQLL
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51
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LGVLTISHQFLVLHPQHDFKILLRLDFLIHDLMIPPNKYFVISRRSFYLLTNYSFKIGKF
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52
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VSWSDITLRHILKGDYLGALEFIESLLQPYCPLANLLKLDNNTEERTKQLMEPFYNLSLA
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53
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ALRFLIKKDNADYNRVYQLLMVVVRVLQQSSKKLDSIPSLDVFLEQGLEFFELKDNAVYF
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54
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EVVANIVAQGSVTSISPVLFRSIIDYYAKEENLKVIEDLIIMLNPTTLDVDLAVKLCQKY
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55
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NLFDLLIYIWNKIFDDYQTPVVDLIYRISNQSEKCVIFNGPQVPPETTIFDYVTYILTGR
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56
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QYPQNLSISPSDKCSKIQRELSAFIFSGFSIKWPSNSNHKLYICENPEEEPAFPYFHLLL
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57
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KSNPSRFLAMLNEVFEASLFNDDNDMVASVGEAELVSRQYVIDLLLDAMKDTGNSDNIRV
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58
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LVAIFIATSISKYPQFIKVSNQALDCVVNTICSSRVQGIYEISQIALESLLPYYHSRTTE
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59
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NFILELKEKNFNKVLFHIYKSENKYASALSLILETKDIEKEYNTDIVSITDYILKKCPPG
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60
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SLECGKVTEVIETNFDLLLSRIGIEKCVTIFSDFDYNLHQEILEVKNEETQQKYLDKLFS
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61
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TPNINNKVDKRLRNLHIELNCKYKSKREMILWLNGTVLSNAESLQILDLLNQDSNFEAAA
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62
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IIHERLESFNLAVRDLLSFIEQCLNEGKTNISTLLESLRRAFDDCNSAGTEKKSCWILLI
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63
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TFLITLYGKYPSHDERKDLCNKLLQEAFLGLVRSKSSSQKDSGGEFWEIMSSVLEHQDVI
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64
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LMKVQDLKQLLLNVFNTYKLERSLSELIQKIIEDSSQDLVQQYRKFLSEGWSIHTDDCEI
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65
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CGKKIWGAGLDPLLFLAWENVQRHQDMISVDLKTPLVIFKCHHGFHQTCLENLAQKPDEY
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66
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SCLICQTESNPKIV
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67
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68
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Found: 5 segments
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69
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70
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Candidate membrane-spanning segments:
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71
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72
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Helix Begin - End Score Certainity
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73
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1 82 - 102 1.209 Certain
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74
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2 266 - 286 1.527 Certain
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75
|
-
3 356 - 376 0.930 Putative
|
|
76
|
-
4 540 - 560 0.810 Putative
|
|
77
|
-
5 1072 - 1092 1.210 Certain
|
|
78
|
-
|
|
79
|
-
Total of 4 structures are to be tested
|
|
80
|
-
|
|
81
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
82
|
-
TOPOLOGY 1 1.00 0.00 0.67 0.00 0.33
|
|
83
|
-
TOPOLOGY ? N-out ?
|
|
84
|
-
LOOP 1 81 81 ( 5.00) 0.91
|
|
85
|
-
TRANSMEM 82 102 21 1.00 1.21
|
|
86
|
-
LOOP 103 265 163 ( 19.00) 1.05
|
|
87
|
-
TRANSMEM 266 286 21 1.00 1.53
|
|
88
|
-
LOOP 287 1071 785 ( 75.00) 0.50
|
|
89
|
-
TRANSMEM 1072 1092 21 1.00 1.21
|
|
90
|
-
LOOP 1093 1274 182 ( 21.00) -0.31
|
|
91
|
-
//
|
|
92
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
93
|
-
TOPOLOGY 2 0.83 0.00 0.57 0.00 0.33
|
|
94
|
-
TOPOLOGY ? N-out ?
|
|
95
|
-
LOOP 1 81 81 ( 5.00) 0.91
|
|
96
|
-
TRANSMEM 82 102 21 1.00 1.21
|
|
97
|
-
LOOP 103 265 163 ( 19.00) 1.05
|
|
98
|
-
TRANSMEM 266 286 21 1.00 1.53
|
|
99
|
-
LOOP 287 355 69 ( 2.00) 1.31
|
|
100
|
-
TRANSMEM 356 376 21 0.83 0.93
|
|
101
|
-
LOOP 377 1071 695 ( 73.00) 0.29
|
|
102
|
-
TRANSMEM 1072 1092 21 1.00 1.21
|
|
103
|
-
LOOP 1093 1274 182 ( 21.00) -0.31
|
|
104
|
-
//
|
|
105
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
106
|
-
TOPOLOGY 3 0.53 0.00 0.31 0.00 0.33
|
|
107
|
-
TOPOLOGY ? N-out ?
|
|
108
|
-
LOOP 1 81 81 ( 5.00) 0.91
|
|
109
|
-
TRANSMEM 82 102 21 1.00 1.21
|
|
110
|
-
LOOP 103 265 163 ( 19.00) 1.05
|
|
111
|
-
TRANSMEM 266 286 21 1.00 1.53
|
|
112
|
-
LOOP 287 539 253 ( 22.00) 0.88
|
|
113
|
-
TRANSMEM 540 560 21 0.53 0.81
|
|
114
|
-
LOOP 561 1071 511 ( 53.00) 0.12
|
|
115
|
-
TRANSMEM 1072 1092 21 1.00 1.21
|
|
116
|
-
LOOP 1093 1274 182 ( 21.00) -0.31
|
|
117
|
-
//
|
|
118
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
119
|
-
TOPOLOGY 4 0.53 0.00 1.30 0.00 0.33
|
|
120
|
-
TOPOLOGY ? N-out ?
|
|
121
|
-
LOOP 1 81 81 ( 5.00) 0.91
|
|
122
|
-
TRANSMEM 82 102 21 1.00 1.21
|
|
123
|
-
LOOP 103 265 163 ( 19.00) 1.05
|
|
124
|
-
TRANSMEM 266 286 21 1.00 1.53
|
|
125
|
-
LOOP 287 355 69 ( 2.00) 1.31
|
|
126
|
-
TRANSMEM 356 376 21 0.83 0.93
|
|
127
|
-
LOOP 377 539 163 ( 20.00) 0.29
|
|
128
|
-
TRANSMEM 540 560 21 0.53 0.81
|
|
129
|
-
LOOP 561 1071 511 ( 53.00) 0.12
|
|
130
|
-
TRANSMEM 1072 1092 21 1.00 1.21
|
|
131
|
-
LOOP 1093 1274 182 ( 21.00) -0.31
|
|
132
|
-
//
|
|
133
|
-
|
|
134
|
-
Sequence : YAL003W (206 res)
|
|
135
|
-
MASTDFSKIETLKQLNASLADKSYIEGTAVSQADVTVFKAFQSAYPEFSRWFNHIASKAD
|
|
136
|
-
EFDSFPAASAAAAEEEEDDDVDLFGSDDEEADAEAEKLKAERIAAYNAKKAAKPAKPAAK
|
|
137
|
-
SIVTLDVKPWDDETNLEEMVANVKAIEMEGLTWGAHQFIPIGFGIKKLQINCVVEDDKVS
|
|
138
|
-
LDDLQQSIEEDEDHVQSTDIAAMQKL
|
|
139
|
-
|
|
140
|
-
Found: 0 segments
|
|
141
|
-
|
|
142
|
-
|
|
143
|
-
Sequence : YAL004W (215 res)
|
|
144
|
-
MGVTSGGLNFKDTVFNEQQRDIESTTTQVENQDVFFLTLLVQTVSNGSGGRFVNNTQDIQ
|
|
145
|
-
TSNGTSILGSLSLRIVEVSWDSDDSVIDLGSQVRFGSFLHLTQDHGGDLFWGKVLGFTLK
|
|
146
|
-
FNLNLRLTVNIDQLEWEVLHVSLHFWVVEVSTDQTLSVENGIRRIHSSLILSSITNQSFS
|
|
147
|
-
VSESDKRWSGSVTLIVGNNVHTIISKVSNTRVCCT
|
|
148
|
-
|
|
149
|
-
Found: 1 segments
|
|
150
|
-
|
|
151
|
-
Candidate membrane-spanning segments:
|
|
152
|
-
|
|
153
|
-
Helix Begin - End Score Certainity
|
|
154
|
-
1 32 - 52 0.624 Putative
|
|
155
|
-
|
|
156
|
-
Total of 2 structures are to be tested
|
|
157
|
-
|
|
158
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
159
|
-
TOPOLOGY 1 0.06 3.00 -0.90 -4.00 0.43
|
|
160
|
-
TOPOLOGY N-in N-in N-out
|
|
161
|
-
CYT_LOOP 1 31 31 2.00 ( 0.28)
|
|
162
|
-
TRANSMEM 32 52 21 0.06 0.62
|
|
163
|
-
EXT_LOOP 53 215 163 ( 12.00) 0.90
|
|
164
|
-
//
|
|
165
|
-
|
|
166
|
-
Sequence : YAL005C (642 res)
|
|
167
|
-
MSKAVGIDLGTTYSCVAHFANDRVDIIANDQGNRTTPSFVAFTDTERLIGDAAKNQAAMN
|
|
168
|
-
PSNTVFDAKRLIGRNFNDPEVQADMKHFPFKLIDVDGKPQIQVEFKGETKNFTPEQISSM
|
|
169
|
-
VLGKMKETAESYLGAKVNDAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIA
|
|
170
|
-
YGLDKKGKEEHVLIFDLGGGTFDVSLLFIEDGIFEVKATAGDTHLGGEDFDNRLVNHFIQ
|
|
171
|
-
EFKRKNKKDLSTNQRALRRLRTACERAKRTLSSSAQTSVEIDSLFEGIDFYTSITRARFE
|
|
172
|
-
ELCADLFRSTLDPVEKVLRDAKLDKSQVDEIVLVGGSTRIPKVQKLVTDYFNGKEPNRSI
|
|
173
|
-
NPDEAVAYGAAVQAAILTGDESSKTQDLLLLDVAPLSLGIETAGGVMTKLIPRNSTISTK
|
|
174
|
-
KFEIFSTYADNQPGVLIQVFEGERAKTKDNNLLGKFELSGIPPAPRGVPQIEVTFDVDSN
|
|
175
|
-
GILNVSAVEKGTGKSNKITITNDKGRLSKEDIEKMVAEAEKFKEEDEKESQRIASKNQLE
|
|
176
|
-
SIAYSLKNTISEAGDKLEQADKDTVTKKAEETISWLDSNTTASKEEFDDKLKELQDIANP
|
|
177
|
-
IMSKLYQAGGAPGGAAGGAPGGFPGGAPPAPEAEGPTVEEVD
|
|
178
|
-
|
|
179
|
-
Found: 2 segments
|
|
180
|
-
|
|
181
|
-
Candidate membrane-spanning segments:
|
|
182
|
-
|
|
183
|
-
Helix Begin - End Score Certainity
|
|
184
|
-
1 388 - 408 0.627 Putative
|
|
185
|
-
2 608 - 628 1.113 Certain
|
|
186
|
-
|
|
187
|
-
Total of 2 structures are to be tested
|
|
188
|
-
|
|
189
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
190
|
-
TOPOLOGY 1 1.00 0.00 0.01 4.00 0.09
|
|
191
|
-
TOPOLOGY ? N-out N-in
|
|
192
|
-
LOOP 1 607 607 ( 79.00) 0.01
|
|
193
|
-
TRANSMEM 608 628 21 1.00 1.11
|
|
194
|
-
LOOP 629 642 14 0.00 ( 0.23)
|
|
195
|
-
//
|
|
196
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
197
|
-
TOPOLOGY 2 0.07 0.00 0.20 -7.00 0.08
|
|
198
|
-
TOPOLOGY ? N-out N-out
|
|
199
|
-
LOOP 1 387 387 ( 49.00) 0.09
|
|
200
|
-
TRANSMEM 388 408 21 0.07 0.63
|
|
201
|
-
LOOP 409 607 199 ( 30.00) -0.10
|
|
202
|
-
TRANSMEM 608 628 21 1.00 1.11
|
|
203
|
-
LOOP 629 642 14 0.00 ( 0.23)
|
|
204
|
-
//
|
|
205
|
-
|
|
206
|
-
Sequence : YAL007C (215 res)
|
|
207
|
-
MIKSTIALPSFFIVLILALVNSVAASSSYAPVAISLPAFSKECLYYDMVTEDDSLAVGYQ
|
|
208
|
-
VLTGGNFEIDFDITAPDGSVITSEKQKKYSDFLLKSFGVGKYTFCFSNNYGTALKKVEIT
|
|
209
|
-
LEKEKTLTDEHEADVNNDDIIANNAVEEIDRNLNKITKTLNYLRAREWRNMSTVNSTESR
|
|
210
|
-
LTWLSILIIIIIAVISIAQVLLIQFLFTGRQKNYV
|
|
211
|
-
|
|
212
|
-
Found: 2 segments
|
|
213
|
-
|
|
214
|
-
Candidate membrane-spanning segments:
|
|
215
|
-
|
|
216
|
-
Helix Begin - End Score Certainity
|
|
217
|
-
1 4 - 24 2.028 Certain
|
|
218
|
-
2 181 - 201 2.276 Certain
|
|
219
|
-
|
|
220
|
-
Total of 1 structures are to be tested
|
|
221
|
-
|
|
222
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
223
|
-
TOPOLOGY 1 1.00 4.00 -0.47 1.00 -1.00
|
|
224
|
-
TOPOLOGY N-in N-in N-in
|
|
225
|
-
CYT_LOOP 1 3 3 1.00 ( -0.18)
|
|
226
|
-
TRANSMEM 4 24 21 1.00 2.03
|
|
227
|
-
EXT_LOOP 25 180 156 ( 17.00) 0.47
|
|
228
|
-
TRANSMEM 181 201 21 1.00 2.28
|
|
229
|
-
CYT_LOOP 202 215 14 2.00 ( 0.42)
|
|
230
|
-
//
|
|
231
|
-
|
|
232
|
-
Sequence : YAL008W (198 res)
|
|
233
|
-
MTLAFNMQRLVFRNLNVGKRMFKNVPLWRFNVANKLGKPLTRSVGLGGAGIVAGGFYLMN
|
|
234
|
-
RQPSKLIFNDSLGAAVKQQGPLEPTVGNSTAITEERRNKISSHKQMFLGSLFGVVLGVTV
|
|
235
|
-
AKISILFMYVGITSMLLCEWLRYKGWIRINLKNIKSVIVLKDVDLKKLLIDGLLGTEYMG
|
|
236
|
-
FKVFFTLSFVLASLNANK
|
|
237
|
-
|
|
238
|
-
Found: 3 segments
|
|
239
|
-
|
|
240
|
-
Candidate membrane-spanning segments:
|
|
241
|
-
|
|
242
|
-
Helix Begin - End Score Certainity
|
|
243
|
-
1 40 - 60 1.208 Certain
|
|
244
|
-
2 121 - 141 1.652 Certain
|
|
245
|
-
3 176 - 196 1.289 Certain
|
|
246
|
-
|
|
247
|
-
Total of 1 structures are to be tested
|
|
248
|
-
|
|
249
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
250
|
-
TOPOLOGY 1 1.00 9.00 0.00 3.00 -1.00
|
|
251
|
-
TOPOLOGY N-in ? N-in
|
|
252
|
-
CYT_LOOP 1 39 39 9.00 ( 0.67)
|
|
253
|
-
TRANSMEM 40 60 21 1.00 1.21
|
|
254
|
-
EXT_LOOP 61 120 60 8.00 ( 1.24)
|
|
255
|
-
TRANSMEM 121 141 21 1.00 1.65
|
|
256
|
-
CYT_LOOP 142 175 34 8.00 ( 0.06)
|
|
257
|
-
TRANSMEM 176 196 21 1.00 1.29
|
|
258
|
-
EXT_LOOP 197 198 2 1.00 ( 0.33)
|
|
259
|
-
//
|
|
260
|
-
|
|
261
|
-
Sequence : YAL009W (259 res)
|
|
262
|
-
MEPESIGDVGNHAQDDSASIVSGPRRRSTSKTSSAKNIRNSSNISPASMIFRNLLILEDD
|
|
263
|
-
LRRQAHEQKILKWQFTLFLASMAGVGAFTFYELYFTSDYVKGLHRVILQFTLSFISITVV
|
|
264
|
-
LFHISGQYRRTIVIPRRFFTSTNKGIRQFNVKLVKVQSTWDEKYTDSVRFVSRTIAYCNI
|
|
265
|
-
YCLKKFLWLKDDNAIVKFWKSVTIQSQPRIGAVDVKLVLNPRAFSAEIREGWEIYRDEFW
|
|
266
|
-
AREGARRRKQAHELRPKSE
|
|
267
|
-
|
|
268
|
-
Found: 2 segments
|
|
269
|
-
|
|
270
|
-
Candidate membrane-spanning segments:
|
|
271
|
-
|
|
272
|
-
Helix Begin - End Score Certainity
|
|
273
|
-
1 73 - 93 1.774 Certain
|
|
274
|
-
2 106 - 126 1.907 Certain
|
|
275
|
-
|
|
276
|
-
Total of 1 structures are to be tested
|
|
277
|
-
|
|
278
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
279
|
-
TOPOLOGY 1 1.00 -2.00 0.28 0.00 -0.10
|
|
280
|
-
TOPOLOGY N-out N-out ?
|
|
281
|
-
EXT_LOOP 1 72 72 ( 11.00) 0.04
|
|
282
|
-
TRANSMEM 73 93 21 1.00 1.77
|
|
283
|
-
CYT_LOOP 94 105 12 2.00 ( 0.89)
|
|
284
|
-
TRANSMEM 106 126 21 1.00 1.91
|
|
285
|
-
EXT_LOOP 127 259 133 ( 28.00) 0.24
|
|
286
|
-
//
|
|
287
|
-
|
|
288
|
-
Sequence : YAL010C (493 res)
|
|
289
|
-
MLPYMDQVLRAFYQSTHWSTQNSYEDITATSRTLLDFRIPSAIHLQISNKSTPNTFNSLD
|
|
290
|
-
FSTRSRINGSLSYLYSDAQQLEKFMRNSTDIPLQDATETYRQLQPNLNFSVSSANTLSSD
|
|
291
|
-
NTTVDNDKKLLHDSKFVKKSLYYGRMYYPSSDLEAMIIKRLSPQTQFMLKGVSSFKESLN
|
|
292
|
-
VLTCYFQRDSHRNLQEWIFSTSDLLCGYRVLHNFLTTPSKFNTSLYNNSSLSLGAEFWLG
|
|
293
|
-
LVSLSPGCSTTLRYYTHSTNTGRPLTLTLSWQPLFGHISSTYSAKTGTNSTFCAKYDFNL
|
|
294
|
-
YSIESNLSFGCEFWQKKHHLLETNKNNNDKLEPISDELVDINPNSRATKLLHENVPDLNS
|
|
295
|
-
AVNDIPSTLDIPVHKQKLLNDLTYAFSSSLRKIDEERSTIEKFDNKINSSIFTSVWKLST
|
|
296
|
-
SLRDKTLKLLWEGKWRGFLISAGTELVFTRGFQESLSDDEKNDNAISISATDTENGNIPV
|
|
297
|
-
FPAKFGIQFQYST
|
|
298
|
-
|
|
299
|
-
Found: 2 segments
|
|
300
|
-
|
|
301
|
-
Candidate membrane-spanning segments:
|
|
302
|
-
|
|
303
|
-
Helix Begin - End Score Certainity
|
|
304
|
-
1 232 - 252 1.181 Certain
|
|
305
|
-
2 264 - 284 0.936 Putative
|
|
306
|
-
|
|
307
|
-
Total of 2 structures are to be tested
|
|
308
|
-
|
|
309
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
310
|
-
TOPOLOGY 1 0.84 -2.00 0.80 -2.00 -0.07
|
|
311
|
-
TOPOLOGY N-out N-out N-out
|
|
312
|
-
EXT_LOOP 1 231 231 ( 23.00) 0.57
|
|
313
|
-
TRANSMEM 232 252 21 1.00 1.18
|
|
314
|
-
CYT_LOOP 253 263 11 2.00 ( 0.31)
|
|
315
|
-
TRANSMEM 264 284 21 0.84 0.94
|
|
316
|
-
EXT_LOOP 285 493 209 ( 24.00) 0.23
|
|
317
|
-
//
|
|
318
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
319
|
-
TOPOLOGY 2 1.00 0.00 0.21 -2.00 -0.07
|
|
320
|
-
TOPOLOGY ? N-out N-out
|
|
321
|
-
LOOP 1 231 231 ( 23.00) 0.57
|
|
322
|
-
TRANSMEM 232 252 21 1.00 1.18
|
|
323
|
-
LOOP 253 493 241 ( 26.00) 0.35
|
|
324
|
-
//
|
|
325
|
-
|
|
326
|
-
Sequence : YAL011W (625 res)
|
|
327
|
-
MPAVLRTRSKESSIEQKPASRTRTRSRRGKRGRDDDDDDDDEESDDAYDEVGNDYDEYAS
|
|
328
|
-
RAKLATNRPFEIVAGLPASVELPNYNSSLTHPQSIKNSGVLYDSLVSSRRTWVQGEMFEL
|
|
329
|
-
YWRRPKKIVSESTPAATESPTSGTIPLIRDKMQKMCDCVMSGGPHTFKVRLFILKNDKIE
|
|
330
|
-
QKWQDEQELKKKEKELKRKNDAEAKRLRMEERKRQQMQKKIAKEQKLQLQKENKAKQKLE
|
|
331
|
-
QEALKLKRKEEMKKLKEQNKNKQGSPSSSMHDPRMIMNLNLMAQEDPKLNTLMETVAKGL
|
|
332
|
-
ANNSQLEEFKKFIEIAKKRSLEENPVNKRPSVTTTRPAPPSKAKDVAEDHRLNSITLVKS
|
|
333
|
-
SKTAATEPEPKKADDENAEKQQSKEAKTTAESTQVDVKKEEEDVKEKGVKSEDTQKKEDN
|
|
334
|
-
QVVPKRKRRKNAIKEDKDMQLTAFQQKYVQGAEIILEYLEFTHSRYYLPKKSVVEFLEDT
|
|
335
|
-
DEIIISWIVIHNSKEIEKFKTKKIKAKLKADQKLNKEDAKPGSDVEKEVSFNPLFEADCP
|
|
336
|
-
TPLYTPMTMKLSGIHKRFNQIIRNSVSPMEEVVKEMEKILQIGTRLSGYNLWYQLDGYDD
|
|
337
|
-
EALSESLRFELNEWEHAMRSRRHKR
|
|
338
|
-
|
|
339
|
-
Found: 0 segments
|
|
340
|
-
|
|
341
|
-
|
|
342
|
-
Sequence : YAL012W (394 res)
|
|
343
|
-
MTLQESDKFATKAIHAGEHVDVHGSVIEPISLSTTFKQSSPANPIGTYEYSRSQNPNREN
|
|
344
|
-
LERAVAALENAQYGLAFSSGSATTATILQSLPQGSHAVSIGDVYGGTHRYFTKVANAHGV
|
|
345
|
-
ETSFTNDLLNDLPQLIKENTKLVWIETPTNPTLKVTDIQKVADLIKKHAAGQDVILVVDN
|
|
346
|
-
TFLSPYISNPLNFGADIVVHSATKYINGHSDVVLGVLATNNKPLYERLQFLQNAIGAIPS
|
|
347
|
-
PFDAWLTHRGLKTLHLRVRQAALSANKIAEFLAADKENVVAVNYPGLKTHPNYDVVLKQH
|
|
348
|
-
RDALGGGMISFRIKGGAEAASKFASSTRLFTLAESLGGIESLLEVPAVMTHGGIPKEARE
|
|
349
|
-
ASGVFDDLVRISVGIEDTDDLLEDIKQALKQATN
|
|
350
|
-
|
|
351
|
-
Found: 1 segments
|
|
352
|
-
|
|
353
|
-
Candidate membrane-spanning segments:
|
|
354
|
-
|
|
355
|
-
Helix Begin - End Score Certainity
|
|
356
|
-
1 72 - 92 1.249 Certain
|
|
357
|
-
|
|
358
|
-
Total of 1 structures are to be tested
|
|
359
|
-
|
|
360
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
361
|
-
TOPOLOGY 1 1.00 0.00 -0.17 0.00 0.20
|
|
362
|
-
TOPOLOGY ? N-in ?
|
|
363
|
-
LOOP 1 71 71 ( 6.00) 0.83
|
|
364
|
-
TRANSMEM 72 92 21 1.00 1.25
|
|
365
|
-
LOOP 93 394 302 ( 29.00) 0.99
|
|
366
|
-
//
|
|
367
|
-
|
|
368
|
-
Sequence : YAL013W (420 res)
|
|
369
|
-
MSQQTPQESEQTTAKEQDLDQESVLSNIDFNTDLNHNLNLSEYCISSDAGTEKMDSDEEK
|
|
370
|
-
SLANLPELKYAPKLSSLVKQETLTESLKRPHEDEKEAIDEAKKMKVPGENEDESKEEEKS
|
|
371
|
-
QELEEAIDSKEKSTDARDEQGDEGDNEEENNEEDNENENEHTAPPALVMPSPIEMEEQRM
|
|
372
|
-
TALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHR
|
|
373
|
-
AYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRDMDIVI
|
|
374
|
-
PDVNYHVPIKLDNKTLSCITGYASAAQLCYPGEPVAEDLACESIEYRYRANPVDKLEVIV
|
|
375
|
-
DRMRLNNEISDLEGLRKYFHSFPGAPELNPLRDSEINDDFHQWAQCDRHTGPHTTSFCYS
|
|
376
|
-
|
|
377
|
-
|
|
378
|
-
Found: 1 segments
|
|
379
|
-
|
|
380
|
-
Candidate membrane-spanning segments:
|
|
381
|
-
|
|
382
|
-
Helix Begin - End Score Certainity
|
|
383
|
-
1 314 - 334 0.632 Putative
|
|
384
|
-
|
|
385
|
-
Total of 2 structures are to be tested
|
|
386
|
-
|
|
387
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
388
|
-
TOPOLOGY 1 0.08 0.00 -0.49 4.00 0.29
|
|
389
|
-
TOPOLOGY ? N-in N-in
|
|
390
|
-
LOOP 1 313 313 ( 40.00) -0.83
|
|
391
|
-
TRANSMEM 314 334 21 0.08 0.63
|
|
392
|
-
LOOP 335 420 86 ( 9.00) -0.34
|
|
393
|
-
//
|
|
394
|
-
|
|
395
|
-
Sequence : YAL014C (255 res)
|
|
396
|
-
MDVLKLGYELDQLSDLVEERTRLVSVLKLAPTSNDNVTLKRQLGSILELLQKCAPNDELI
|
|
397
|
-
SRYNTILDKIPDTAVDKELYRFQQQVARNTDEVSKESLKKVRFKNDDELTVMYKDDDEQD
|
|
398
|
-
EESPLPSTHTPYKDEPLQSQLQSQSQPQPPQPMVSNQELFINQQQQLLEQDSHLGALSQS
|
|
399
|
-
IGRTHDISLDLNNEIVSQNDSLLVDLENLIDNNGRNLNRASRSMHGFNNSRFKDNGNCVI
|
|
400
|
-
ILVLIVVLLLLLLVL
|
|
401
|
-
|
|
402
|
-
Found: 1 segments
|
|
403
|
-
|
|
404
|
-
Candidate membrane-spanning segments:
|
|
405
|
-
|
|
406
|
-
Helix Begin - End Score Certainity
|
|
407
|
-
1 235 - 255 2.417 Certain
|
|
408
|
-
|
|
409
|
-
Total of 1 structures are to be tested
|
|
410
|
-
|
|
411
|
-
HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
|
|
412
|
-
TOPOLOGY 1 1.00 0.00 -0.09 2.00 0.23
|
|
413
|
-
TOPOLOGY ? N-in N-in
|
|
414
|
-
LOOP 1 234 234 ( 25.00) -0.09
|
|
415
|
-
TRANSMEM 235 255 21 1.00 2.42
|
|
416
|
-
//
|