SPAT (Soft PATtern discovery)

 

1. Options of the program spat_cli.php -infile pools.fasta -problem rspd -order sc -minslack 0 -maxslack 9 2. Summary of the data         Data file: single line format   pools.txt       Fasta format   pools.fasta  Données Nombre Longueur_min Longueur_max Moyenne Global 102 75 742 181.58 classe 1 24 86 249 180.42 classe 2 47 87 742 184.51 classe 3 31 75 420 178.03 3. 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 Characterization complete for class 1. 3.5 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 4 Characterization complete for class 1 (already known from step maxSlack=3). 3.6 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 5 Characterization complete for class 1 (already known from step maxSlack=3). 3.7 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 6 Characterization complete for class 1 (already known from step maxSlack=3). 3.8 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 7 Characterization complete for class 1 (already known from step maxSlack=3). 3.9 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 8 Characterization complete for class 1 (already known from step maxSlack=3). 3.10 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 9 Characterization complete for class 1 (already known from step maxSlack=3). 4. Characterization of the classes over the 10 step(s) Correspondence between class number and class description Class number Class description 1 pool One = hydrophylin-like LEAPs 2 pool Two = control LEAPs 3 pool Three = hydrophilins   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 ok 24      step 3 2 2 2 0 EKK KK GE G...K..E K...K..G ok 1 2 unsat 47      unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat 2 3 unsat 31      unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat 3 The positions of the motifs can be read in the xml file:  pools.xml  Elapsed time: 6.7 seconds.

 

 

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