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SPAT (Soft PATtern discovery)

 

1. Options of the program

spat_cli.php -infile sets.fasta -problem rspd -order sc -minslack 0 -maxslack 9  

2. 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    102.61

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

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)

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 

Elapsed time: 34.2 seconds.

 

 

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