mspire 0.4.9 → 0.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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Cutoff for putative transmembrane segments: 0.60
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Critical distance between 2 transmembrane segments: 2
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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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VYCDGAITTKNVTDIIGDANHSYSVGITEDSLWTLLTGYTKKESTIGNSAFELLLEVAKS
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GEKGINTMDLAQVTGQDPRSVTGRIKKINHLLTSSQLIYKGHVVKQLKLKKFSHDGVDSN
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PYINIRDHLATIVEVVKRSKNGIRQIIDLKRELKFDKEKRLSKAFIAAIAWLDEKEYLKK
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VLVVSPKNPAIKIRCVKYVKDIPDSKGSPSFEYDSNSADEDSVSDSKAAFEDEDLVEGLD
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NFNATDLLQNQGLVMEEKEDAVKNEVLLNRFYPLQNQTYDIADKSGLKGISTMDVVNRIT
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GKEFQRAFTKSSEYYLESVDKQKENTGGYRLFRIYDFEGKKKFFRLFTAQNFQKLTNAED
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EISVPKGFDELGKSRTDLKTLNEDNFVALNNTVRFTTDSDGQDIFFWHGELKIPPNSKKT
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PNKNKRKRQVKNSTNASVAGNISNPKRIKLEQHVSTAQEPKSAEDSPSSNGGTVVKGKVV
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NFGGFSARSLRSLQRQRAILKVMNTIGGVAYLREQFYESVSKYMGSTTTLDKKTVRGDVD
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LMVESEKLGARTEPVSGRKIIFLPTVGEDAIQRYILKEKDSKKATFTDVIHDTEIYFFDQ
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TEKNRFHRGKKSVERIRKFQNRQKNAKIKASDDAISKKSTSVNVSDGKIKRRDKKVSAGR
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TTVVVENTKEDKTVYHAGTKDGVQALIRAVVVTKSIKNEIMWDKITKLFPNNSLDNLKKK
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WTARRVRMGHSGWRAYVDKWKKMLVLAIKSEKISLRDVEELDLIKLLDIWTSFDEKEIKR
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PLFLYKNYEENRKKFTLVRDDTLTHSGNDLAMSSMIQREISSLKKTYTRKISASTKDLSK
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SQSDDYIRTVIRSILIESPSTTRNEIEALKNVGNESIDNVIMDMAKEKQIYLHGSKLECT
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DTLPDILENRGNYKDFGVAFQYRCKVNELLEAGNAIVINQEPSDISSWVLIDLISGELLN
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MDVIPMVRNVRPLTYTSRRFEIRTLTPPLIIYANSQTKLNTARKSAVKVPLGKPFSRLWV
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NGSGSIRPNIWKQVVTMVVNEIIFHPGITLSRLQSRCREVLSLHEISEICKWLLERQVLI
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Sequence : YAL002W (1274 res)
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MEQNGLDHDSRSSIDTTINDTQKTFLEFRSYTQLSEKLASSSSYTAPPLNEDGPKGVASA
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VSQGSESVVSWTTLTHVYSILGAYGGPTCLYPTATYFLMGTSKGCVLIFNYNEHLQTILV
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PTLSEDPSIHSIRSPVKSIVICSDGTHVAASYETGNICIWNLNVGYRVKPTSEPTNGMTP
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TPALPAVLHIDDHVNKEITGLDFFGARHTALIVSDRTGKVSLYNGYRRGFWQLVYNSKKI
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LDVNSSKEKLIRSKLSPLISREKISTNLLSVLTTTHFALILLSPHVSLMFQETVEPSVQN
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SLVVNSSISWTQNCSRVAYSVNNKISVISISSSDFNVQSASHSPEFAESILSIQWIDQLL
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LGVLTISHQFLVLHPQHDFKILLRLDFLIHDLMIPPNKYFVISRRSFYLLTNYSFKIGKF
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VSWSDITLRHILKGDYLGALEFIESLLQPYCPLANLLKLDNNTEERTKQLMEPFYNLSLA
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ALRFLIKKDNADYNRVYQLLMVVVRVLQQSSKKLDSIPSLDVFLEQGLEFFELKDNAVYF
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EVVANIVAQGSVTSISPVLFRSIIDYYAKEENLKVIEDLIIMLNPTTLDVDLAVKLCQKY
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NLFDLLIYIWNKIFDDYQTPVVDLIYRISNQSEKCVIFNGPQVPPETTIFDYVTYILTGR
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QYPQNLSISPSDKCSKIQRELSAFIFSGFSIKWPSNSNHKLYICENPEEEPAFPYFHLLL
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KSNPSRFLAMLNEVFEASLFNDDNDMVASVGEAELVSRQYVIDLLLDAMKDTGNSDNIRV
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LVAIFIATSISKYPQFIKVSNQALDCVVNTICSSRVQGIYEISQIALESLLPYYHSRTTE
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NFILELKEKNFNKVLFHIYKSENKYASALSLILETKDIEKEYNTDIVSITDYILKKCPPG
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SLECGKVTEVIETNFDLLLSRIGIEKCVTIFSDFDYNLHQEILEVKNEETQQKYLDKLFS
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TPNINNKVDKRLRNLHIELNCKYKSKREMILWLNGTVLSNAESLQILDLLNQDSNFEAAA
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IIHERLESFNLAVRDLLSFIEQCLNEGKTNISTLLESLRRAFDDCNSAGTEKKSCWILLI
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TFLITLYGKYPSHDERKDLCNKLLQEAFLGLVRSKSSSQKDSGGEFWEIMSSVLEHQDVI
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LMKVQDLKQLLLNVFNTYKLERSLSELIQKIIEDSSQDLVQQYRKFLSEGWSIHTDDCEI
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CGKKIWGAGLDPLLFLAWENVQRHQDMISVDLKTPLVIFKCHHGFHQTCLENLAQKPDEY
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SCLICQTESNPKIV
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Found: 5 segments
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Candidate membrane-spanning segments:
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Helix Begin - End Score Certainity
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1 82 - 102 1.209 Certain
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|
-
2 266 - 286 1.527 Certain
|
|
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
|
-
//
|