Valid XHTML     Valid CSS2    

SPAT (Soft PATtern discovery)

 

1. Options of the program

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

2. 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    214.86

3. 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)

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 

Elapsed time: 112.1 seconds.

 

 

retour gH    Retour à la page principale de   (gH)