SPAT (Soft PATtern discovery)
1. Options of the program
spat_cli.php -infile shspdb.fasta -problem rspd -order sc -minslack 0 -maxslack 92. Summary of the data
Data file: single line format shspdb.txt Fasta format shspdb.fasta
Données Nombre Longueur_min Longueur_max Moyenne Global 2330 79 498 176.72 classe 1 247 130 163 155.37 classe 20 96 214 298 278.21 classe 16 31 114 154 141.26 classe 13 120 174 271 211.39 classe 12 258 128 269 184.34 classe 6 66 127 248 213.11 classe 2 107 129 174 156.08 classe 19 23 194 220 210.87 classe 7 80 163 266 235.53 classe 3 47 165 328 198.40 classe 23 26 79 127 103.69 classe 11 314 124 340 160.70 classe 10 311 120 498 158.31 classe 18 155 107 277 148.62 classe 8 15 115 146 140.20 classe 5 14 172 203 190.93 classe 21 102 161 344 294.21 classe 15 25 108 262 176.80 classe 4 16 119 173 139.12 classe 17 75 102 131 106.35 classe 9 164 121 170 134.16 classe 14 25 145 178 151.92 classe 22 13 332 453 381.463. Analysis of the data
3.1 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 0
Characterization complete for class 4.
Characterization complete for class 5.
Characterization complete for class 14.
Characterization complete for class 15.
Characterization complete for class 16.
Characterization complete for class 17.
Characterization complete for class 22.
3.2 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 1
Characterization complete for class 4 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=0).
Characterization complete for class 8.
Characterization complete for class 13.
Characterization complete for class 14 (already known from step maxSlack=0).
Characterization complete for class 15 (already known from step maxSlack=0).
Characterization complete for class 16 (already known from step maxSlack=0).
Characterization complete for class 17 (already known from step maxSlack=0).
Characterization complete for class 19.
Characterization complete for class 21.
Characterization complete for class 22 (already known from step maxSlack=0).
Characterization complete for class 23.
3.3 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 2
Characterization complete for class 2.
Characterization complete for class 4 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=0).
Characterization complete for class 8 (already known from step maxSlack=1).
Characterization complete for class 9.
Characterization complete for class 13 (already known from step maxSlack=1).
Characterization complete for class 14 (already known from step maxSlack=0).
Characterization complete for class 15 (already known from step maxSlack=0).
Characterization complete for class 16 (already known from step maxSlack=0).
Characterization complete for class 17 (already known from step maxSlack=0).
Characterization complete for class 19 (already known from step maxSlack=1).
Characterization complete for class 21 (already known from step maxSlack=1).
Characterization complete for class 22 (already known from step maxSlack=0).
Characterization complete for class 23 (already known from step maxSlack=1).
3.4 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 3
Characterization complete for class 2 (already known from step maxSlack=2).
Characterization complete for class 3.
Characterization complete for class 4 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=0).
Characterization complete for class 7.
Characterization complete for class 8 (already known from step maxSlack=1).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 13 (already known from step maxSlack=1).
Characterization complete for class 14 (already known from step maxSlack=0).
Characterization complete for class 15 (already known from step maxSlack=0).
Characterization complete for class 16 (already known from step maxSlack=0).
Characterization complete for class 17 (already known from step maxSlack=0).
Characterization complete for class 19 (already known from step maxSlack=1).
Characterization complete for class 20.
Characterization complete for class 21 (already known from step maxSlack=1).
Characterization complete for class 22 (already known from step maxSlack=0).
Characterization complete for class 23 (already known from step maxSlack=1).
3.5 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 4
Characterization complete for class 2 (already known from step maxSlack=2).
Characterization complete for class 3 (already known from step maxSlack=3).
Characterization complete for class 4 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=0).
Characterization complete for class 7 (already known from step maxSlack=3).
Characterization complete for class 8 (already known from step maxSlack=1).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 13 (already known from step maxSlack=1).
Characterization complete for class 14 (already known from step maxSlack=0).
Characterization complete for class 15 (already known from step maxSlack=0).
Characterization complete for class 16 (already known from step maxSlack=0).
Characterization complete for class 17 (already known from step maxSlack=0).
Characterization complete for class 19 (already known from step maxSlack=1).
Characterization complete for class 20 (already known from step maxSlack=3).
Characterization complete for class 21 (already known from step maxSlack=1).
Characterization complete for class 22 (already known from step maxSlack=0).
Characterization complete for class 23 (already known from step maxSlack=1).
3.6 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 5
Characterization complete for class 2 (already known from step maxSlack=2).
Characterization complete for class 3 (already known from step maxSlack=3).
Characterization complete for class 4 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=0).
Characterization complete for class 7 (already known from step maxSlack=3).
Characterization complete for class 8 (already known from step maxSlack=1).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 13 (already known from step maxSlack=1).
Characterization complete for class 14 (already known from step maxSlack=0).
Characterization complete for class 15 (already known from step maxSlack=0).
Characterization complete for class 16 (already known from step maxSlack=0).
Characterization complete for class 17 (already known from step maxSlack=0).
Characterization complete for class 19 (already known from step maxSlack=1).
Characterization complete for class 20 (already known from step maxSlack=3).
Characterization complete for class 21 (already known from step maxSlack=1).
Characterization complete for class 22 (already known from step maxSlack=0).
Characterization complete for class 23 (already known from step maxSlack=1).
3.7 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 6
Characterization complete for class 2 (already known from step maxSlack=2).
Characterization complete for class 3 (already known from step maxSlack=3).
Characterization complete for class 4 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=0).
Characterization complete for class 7 (already known from step maxSlack=3).
Characterization complete for class 8 (already known from step maxSlack=1).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 13 (already known from step maxSlack=1).
Characterization complete for class 14 (already known from step maxSlack=0).
Characterization complete for class 15 (already known from step maxSlack=0).
Characterization complete for class 16 (already known from step maxSlack=0).
Characterization complete for class 17 (already known from step maxSlack=0).
Characterization complete for class 19 (already known from step maxSlack=1).
Characterization complete for class 20 (already known from step maxSlack=3).
Characterization complete for class 21 (already known from step maxSlack=1).
Characterization complete for class 22 (already known from step maxSlack=0).
Characterization complete for class 23 (already known from step maxSlack=1).
3.8 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 7
Characterization complete for class 2 (already known from step maxSlack=2).
Characterization complete for class 3 (already known from step maxSlack=3).
Characterization complete for class 4 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=0).
Characterization complete for class 7 (already known from step maxSlack=3).
Characterization complete for class 8 (already known from step maxSlack=1).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 13 (already known from step maxSlack=1).
Characterization complete for class 14 (already known from step maxSlack=0).
Characterization complete for class 15 (already known from step maxSlack=0).
Characterization complete for class 16 (already known from step maxSlack=0).
Characterization complete for class 17 (already known from step maxSlack=0).
Characterization complete for class 19 (already known from step maxSlack=1).
Characterization complete for class 20 (already known from step maxSlack=3).
Characterization complete for class 21 (already known from step maxSlack=1).
Characterization complete for class 22 (already known from step maxSlack=0).
Characterization complete for class 23 (already known from step maxSlack=1).
3.9 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 8
Characterization complete for class 2 (already known from step maxSlack=2).
Characterization complete for class 3 (already known from step maxSlack=3).
Characterization complete for class 4 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=0).
Characterization complete for class 6.
Characterization complete for class 7 (already known from step maxSlack=3).
Characterization complete for class 8 (already known from step maxSlack=1).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 13 (already known from step maxSlack=1).
Characterization complete for class 14 (already known from step maxSlack=0).
Characterization complete for class 15 (already known from step maxSlack=0).
Characterization complete for class 16 (already known from step maxSlack=0).
Characterization complete for class 17 (already known from step maxSlack=0).
Characterization complete for class 19 (already known from step maxSlack=1).
Characterization complete for class 20 (already known from step maxSlack=3).
Characterization complete for class 21 (already known from step maxSlack=1).
Characterization complete for class 22 (already known from step maxSlack=0).
Characterization complete for class 23 (already known from step maxSlack=1).
3.10 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 9
Characterization complete for class 2 (already known from step maxSlack=2).
Characterization complete for class 3 (already known from step maxSlack=3).
Characterization complete for class 4 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=0).
Characterization complete for class 6 (already known from step maxSlack=8).
Characterization complete for class 7 (already known from step maxSlack=3).
Characterization complete for class 8 (already known from step maxSlack=1).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 13 (already known from step maxSlack=1).
Characterization complete for class 14 (already known from step maxSlack=0).
Characterization complete for class 15 (already known from step maxSlack=0).
Characterization complete for class 16 (already known from step maxSlack=0).
Characterization complete for class 17 (already known from step maxSlack=0).
Characterization complete for class 19 (already known from step maxSlack=1).
Characterization complete for class 20 (already known from step maxSlack=3).
Characterization complete for class 21 (already known from step maxSlack=1).
Characterization complete for class 22 (already known from step maxSlack=0).
Characterization complete for class 23 (already known from step maxSlack=1).
4. Characterization of the classes over the 10 step(s)
Elapsed time: 299.5 seconds.Correspondence between class number and class description
Class number Class description 1 sHSP database class 1 2 sHSP database class 2 3 sHSP database class 3 4 sHSP database class 4 5 sHSP database class 5 6 sHSP database class 6 7 sHSP database class 7 8 sHSP database class 8 9 sHSP database class 9 10 sHSP database class 10 11 sHSP database class 11 12 sHSP database class 12 13 sHSP database class 13 14 sHSP database class 14 15 sHSP database class 15 16 sHSP database class 16 17 sHSP database class 17 18 sHSP database class 18 19 sHSP database class 19 20 sHSP database class 20 21 sHSP database class 21 22 sHSP database class 22 23 sHSP database class 23
Results of the characterization program
It was not possible to solve all the classes. Here are the partial solutions:
Class Statut Proteins When NonExp Motif(s) step 0 step 1 (new) step 2 (new) step 3 (new) step 4 (new) step 5 (new) step 6 (new) step 7 (new) step 8 (new) step 9 (new) Statut Class 1 sat 247 632 126 40 40 40 20 7 5 3 2 ET SG V.V E.G V.K E..V E..K R..E R..R E.....V V.....P G.....V G.....F A....G......P K......V V......G D......E A.......E D........V E........A V......K E.........D R.........R sat 1 2 ok 107 step 2 41 10 0 LP PG ER VL KF PE PP D.P I.V V.V G.R R.E KF..P K..P ok 2 3 ok 47 step 3 185 177 1 0 GER VL PF GV DW WH ER RV DW.ET L.V D.F G.L E.E G..W A..D P...D P...L ok 3 4 ok 16 step 0 0 RKFRLP YL AR ok 4 5 ok 14 step 0 0 PLW VDW ok 5 6 ok 66 step 8 232 60 38 11 9 2 2 2 0 GVL GL PG KE VK IK S.R L.I E.K K.G N..L L..K G..K K..V K...K..V L...M M....L L.....G R.....L V.....E L........L ok 6 7 ok 80 step 3 25 3 2 0 DV PW MP PG KE ED VK AE PK K.R V.D D.P E..K R...PG F...G ok 7 8 ok 15 step 1 1 0 VPG DW KD VK PK SK DW.E K.Q I.V NV ok 8 9 ok 164 step 2 546 63 0 TR RR R.D P.K A.R R..A..A P.K..R R..K ok 9 10 sat 311 1792 1792 1792 1792 1792 1792 1792 1792 1792 unsat G.L sat 10 11 unsat 314 unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat 11 12 sat 258 1025 1025 1025 1025 1025 606 243 unsat unsat unsat R...R R........P S.........P sat 12 13 ok 120 step 1 111 0 RG FQ QG RG.Q F.G W.G ok 13 14 ok 25 step 0 0 ALPGP ok 14 15 ok 25 step 0 0 FRTEIKI ok 15 16 ok 31 step 0 0 PQEF ok 16 17 ok 75 step 0 0 PWY LG AE ok 17 18 sat 155 79 79 79 79 79 79 79 79 79 79 CN sat 18 19 ok 23 step 1 1 0 AE ET LS FS PE PE CS EG PE.V S.K Q.S ok 19 20 ok 96 step 3 94 43 12 0 LL TG GF AG GG P.G P.S L..L E..L F...G A...L G...L T...P ok 20 21 ok 102 step 1 989 0 EQ V.L E.L C.C ok 21 22 ok 13 step 0 0 DEEL SKP ok 22 23 ok 26 step 1 1 0 MSD KA KE DK K.F ok 23 Class Statut Proteins When NonExp Motif(s) step 0 step 1 (new) step 2 (new) step 3 (new) step 4 (new) step 5 (new) step 6 (new) step 7 (new) step 8 (new) step 9 (new) Statut Class The positions of the motifs can be read in the xml file: shspdb.xml
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