SPAT (Soft PATtern discovery)
1. Options of the program
spat_cli.php -infile leadb.fasta -problem rspd -order sc -minslack 0 -maxslack 92. Summary of the data
Data file: single line format leadb.txt Fasta format leadb.fasta
Données Nombre Longueur_min Longueur_max Moyenne Global 1139 66 843 195.48 classe 5 60 83 217 108.72 classe 7 57 95 341 171.74 classe 6 213 66 843 245.76 classe 1 200 117 507 190.53 classe 9 67 78 144 98.81 classe 4 92 81 625 225.49 classe 2 98 122 338 225.84 classe 10 76 88 173 144.50 classe 3 29 86 186 121.28 classe 12 15 71 117 94.27 classe 11 24 159 278 241.17 classe 8 208 136 411 214.863. Analysis of the data
3.1 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 0
Characterization complete for class 3.
Characterization complete for class 12.
3.2 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 1
Characterization complete for class 3 (already known from step maxSlack=0).
Characterization complete for class 11.
Characterization complete for class 12 (already known from step maxSlack=0).
3.3 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 2
Characterization complete for class 3 (already known from step maxSlack=0).
Characterization complete for class 5.
Characterization complete for class 9.
Characterization complete for class 11 (already known from step maxSlack=1).
Characterization complete for class 12 (already known from step maxSlack=0).
3.4 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 3
Characterization complete for class 3 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=2).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 11 (already known from step maxSlack=1).
Characterization complete for class 12 (already known from step maxSlack=0).
3.5 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 4
Characterization complete for class 3 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=2).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 11 (already known from step maxSlack=1).
Characterization complete for class 12 (already known from step maxSlack=0).
3.6 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 5
Characterization complete for class 3 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=2).
Characterization complete for class 7.
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 11 (already known from step maxSlack=1).
Characterization complete for class 12 (already known from step maxSlack=0).
3.7 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 6
Characterization complete for class 3 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=2).
Characterization complete for class 7 (already known from step maxSlack=5).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 11 (already known from step maxSlack=1).
Characterization complete for class 12 (already known from step maxSlack=0).
3.8 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 7
Characterization complete for class 3 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=2).
Characterization complete for class 7 (already known from step maxSlack=5).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 11 (already known from step maxSlack=1).
Characterization complete for class 12 (already known from step maxSlack=0).
3.9 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 8
Characterization complete for class 3 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=2).
Characterization complete for class 7 (already known from step maxSlack=5).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 11 (already known from step maxSlack=1).
Characterization complete for class 12 (already known from step maxSlack=0).
3.10 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 9
Characterization complete for class 3 (already known from step maxSlack=0).
Characterization complete for class 5 (already known from step maxSlack=2).
Characterization complete for class 7 (already known from step maxSlack=5).
Characterization complete for class 9 (already known from step maxSlack=2).
Characterization complete for class 11 (already known from step maxSlack=1).
Characterization complete for class 12 (already known from step maxSlack=0).
4. Characterization of the classes over the 10 step(s)
Elapsed time: 112.1 seconds.Correspondence between class number and class description
Class number Class description 1 LEAP database class 1 2 LEAP database class 2 3 LEAP database class 3 4 LEAP database class 4 5 LEAP database class 5 6 LEAP database class 6 7 LEAP database class 7 8 LEAP database class 8 9 LEAP database class 9 10 LEAP database class 10 11 LEAP database class 11 12 LEAP database class 12
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 200 131 126 119 117 96 94 92 89 89 89 SSS KK PG KG KI K.P K.K K.K E..G K...K K....K...K E....G KG.....K.K G.....K K......I S.......G sat 1 2 sat 98 166 157 148 44 19 19 19 12 11 11 SSSS KLPG KL K.K.KLPG S.SSS K.K K.K E.K EK..G S..D G..K KEK EK G...K.K.KLPG E...K G...K G...K E....K D....K K.......S K........H sat 2 3 ok 29 step 0 0 SSSDSD ok 3 4 sat 92 731 731 731 731 731 731 731 unsat unsat unsat G...K sat 4 5 ok 60 step 2 11 5 0 RA GG GG EG GG EQ EG G.K G.Q G..R..Q G..GG A..E ok 5 6 unsat 213 unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat 6 7 ok 57 step 5 5 5 5 5 5 0 NPY IP A.....D ok 7 8 sat 208 365 90 90 90 90 90 90 90 90 90 NP N.N sat 8 9 ok 67 step 2 270 270 0 DP W..DP..G ok 9 10 sat 76 205 149 143 63 60 60 54 46 25 21 AA AK KA EK AE KE KE K.A A.A E.A K..A A..K M...K A...A A...E A....K K....E K......K K......K A......E A..K.......A A........A E........K KE.........K A.........KA sat 10 11 ok 24 step 1 8 0 AAE AAA AL GG GG GV VT AE DA.A GG.A E.L P.G ok 11 12 ok 15 step 0 0 EDYK PY ok 12 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: leadb.xml
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