SPAT (Soft PATtern discovery)
1. Options of the program
spat_cli.php -infile sets.fasta -problem rspd -order sc -minslack 0 -maxslack 92. Summary of the data
Data file: single line format sets.txt Fasta format sets.fasta
Données Nombre Longueur_min Longueur_max Moyenne Global 470 86 411 177.25 classe 1 24 86 249 180.42 classe 2 96 122 338 225.67 classe 3 186 95 411 217.67 classe 4 164 100 246 102.613. Analysis of the data
3.1 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 0
3.2 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 1
3.3 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 2
3.4 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 3
3.5 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 4
3.6 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 5
3.7 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 6
3.8 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 7
3.9 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 8
3.10 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 9
4. Characterization of the classes over the 10 step(s)
Elapsed time: 34.2 seconds.Correspondence between class number and class description
Class number Class description 1 pool One = hydrophylin-like LEAPs 2 LEAPdb class 2 3 LEAPdb class 8 4 WHy domain proteins
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 24 104 102 97 65 57 45 43 41 30 27 EKK EE GE K.E K.G K..E K..E E..K E..E G...K..E K.G...K K...KK E..K....K G....E E....E E...K.....K G.....E K.....E K.....E G......K D......K K.......G E.......D G........KK K........G G........K K........K K........K K........K G.........E sat 1 2 sat 96 18 18 17 17 17 17 17 17 17 17 KLPG K.K.KLPG S..D sat 2 3 unsat 186 unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat 3 4 sat 164 195 195 195 195 195 195 195 195 195 unsat N.N sat 4 The positions of the motifs can be read in the xml file: sets.xml
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