Valid XHTML     Valid CSS2    

SPAT (Soft PATtern discovery)

 

1. Options of the program

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

2. Summary of the data

        Data file: single line format   shspdb.txt       Fasta format   shspdb.fasta 

Données         Nombre   Longueur_min Longueur_max   Moyenne  
  Global          2330             79          498    176.72
  classe   1       247            130          163    155.37
  classe  20        96            214          298    278.21
  classe  16        31            114          154    141.26
  classe  13       120            174          271    211.39
  classe  12       258            128          269    184.34
  classe   6        66            127          248    213.11
  classe   2       107            129          174    156.08
  classe  19        23            194          220    210.87
  classe   7        80            163          266    235.53
  classe   3        47            165          328    198.40
  classe  23        26             79          127    103.69
  classe  11       314            124          340    160.70
  classe  10       311            120          498    158.31
  classe  18       155            107          277    148.62
  classe   8        15            115          146    140.20
  classe   5        14            172          203    190.93
  classe  21       102            161          344    294.21
  classe  15        25            108          262    176.80
  classe   4        16            119          173    139.12
  classe  17        75            102          131    106.35
  classe   9       164            121          170    134.16
  classe  14        25            145          178    151.92
  classe  22        13            332          453    381.46

3. Analysis of the data

3.1 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 0

Characterization complete for class 4.

Characterization complete for class 5.

Characterization complete for class 14.

Characterization complete for class 15.

Characterization complete for class 16.

Characterization complete for class 17.

Characterization complete for class 22.

3.2 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 1

Characterization complete for class 4 (already known from step maxSlack=0).

Characterization complete for class 5 (already known from step maxSlack=0).

Characterization complete for class 8.

Characterization complete for class 13.

Characterization complete for class 14 (already known from step maxSlack=0).

Characterization complete for class 15 (already known from step maxSlack=0).

Characterization complete for class 16 (already known from step maxSlack=0).

Characterization complete for class 17 (already known from step maxSlack=0).

Characterization complete for class 19.

Characterization complete for class 21.

Characterization complete for class 22 (already known from step maxSlack=0).

Characterization complete for class 23.

3.3 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 2

Characterization complete for class 2.

Characterization complete for class 4 (already known from step maxSlack=0).

Characterization complete for class 5 (already known from step maxSlack=0).

Characterization complete for class 8 (already known from step maxSlack=1).

Characterization complete for class 9.

Characterization complete for class 13 (already known from step maxSlack=1).

Characterization complete for class 14 (already known from step maxSlack=0).

Characterization complete for class 15 (already known from step maxSlack=0).

Characterization complete for class 16 (already known from step maxSlack=0).

Characterization complete for class 17 (already known from step maxSlack=0).

Characterization complete for class 19 (already known from step maxSlack=1).

Characterization complete for class 21 (already known from step maxSlack=1).

Characterization complete for class 22 (already known from step maxSlack=0).

Characterization complete for class 23 (already known from step maxSlack=1).

3.4 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 3

Characterization complete for class 2 (already known from step maxSlack=2).

Characterization complete for class 3.

Characterization complete for class 4 (already known from step maxSlack=0).

Characterization complete for class 5 (already known from step maxSlack=0).

Characterization complete for class 7.

Characterization complete for class 8 (already known from step maxSlack=1).

Characterization complete for class 9 (already known from step maxSlack=2).

Characterization complete for class 13 (already known from step maxSlack=1).

Characterization complete for class 14 (already known from step maxSlack=0).

Characterization complete for class 15 (already known from step maxSlack=0).

Characterization complete for class 16 (already known from step maxSlack=0).

Characterization complete for class 17 (already known from step maxSlack=0).

Characterization complete for class 19 (already known from step maxSlack=1).

Characterization complete for class 20.

Characterization complete for class 21 (already known from step maxSlack=1).

Characterization complete for class 22 (already known from step maxSlack=0).

Characterization complete for class 23 (already known from step maxSlack=1).

3.5 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 4

Characterization complete for class 2 (already known from step maxSlack=2).

Characterization complete for class 3 (already known from step maxSlack=3).

Characterization complete for class 4 (already known from step maxSlack=0).

Characterization complete for class 5 (already known from step maxSlack=0).

Characterization complete for class 7 (already known from step maxSlack=3).

Characterization complete for class 8 (already known from step maxSlack=1).

Characterization complete for class 9 (already known from step maxSlack=2).

Characterization complete for class 13 (already known from step maxSlack=1).

Characterization complete for class 14 (already known from step maxSlack=0).

Characterization complete for class 15 (already known from step maxSlack=0).

Characterization complete for class 16 (already known from step maxSlack=0).

Characterization complete for class 17 (already known from step maxSlack=0).

Characterization complete for class 19 (already known from step maxSlack=1).

Characterization complete for class 20 (already known from step maxSlack=3).

Characterization complete for class 21 (already known from step maxSlack=1).

Characterization complete for class 22 (already known from step maxSlack=0).

Characterization complete for class 23 (already known from step maxSlack=1).

3.6 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 5

Characterization complete for class 2 (already known from step maxSlack=2).

Characterization complete for class 3 (already known from step maxSlack=3).

Characterization complete for class 4 (already known from step maxSlack=0).

Characterization complete for class 5 (already known from step maxSlack=0).

Characterization complete for class 7 (already known from step maxSlack=3).

Characterization complete for class 8 (already known from step maxSlack=1).

Characterization complete for class 9 (already known from step maxSlack=2).

Characterization complete for class 13 (already known from step maxSlack=1).

Characterization complete for class 14 (already known from step maxSlack=0).

Characterization complete for class 15 (already known from step maxSlack=0).

Characterization complete for class 16 (already known from step maxSlack=0).

Characterization complete for class 17 (already known from step maxSlack=0).

Characterization complete for class 19 (already known from step maxSlack=1).

Characterization complete for class 20 (already known from step maxSlack=3).

Characterization complete for class 21 (already known from step maxSlack=1).

Characterization complete for class 22 (already known from step maxSlack=0).

Characterization complete for class 23 (already known from step maxSlack=1).

3.7 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 6

Characterization complete for class 2 (already known from step maxSlack=2).

Characterization complete for class 3 (already known from step maxSlack=3).

Characterization complete for class 4 (already known from step maxSlack=0).

Characterization complete for class 5 (already known from step maxSlack=0).

Characterization complete for class 7 (already known from step maxSlack=3).

Characterization complete for class 8 (already known from step maxSlack=1).

Characterization complete for class 9 (already known from step maxSlack=2).

Characterization complete for class 13 (already known from step maxSlack=1).

Characterization complete for class 14 (already known from step maxSlack=0).

Characterization complete for class 15 (already known from step maxSlack=0).

Characterization complete for class 16 (already known from step maxSlack=0).

Characterization complete for class 17 (already known from step maxSlack=0).

Characterization complete for class 19 (already known from step maxSlack=1).

Characterization complete for class 20 (already known from step maxSlack=3).

Characterization complete for class 21 (already known from step maxSlack=1).

Characterization complete for class 22 (already known from step maxSlack=0).

Characterization complete for class 23 (already known from step maxSlack=1).

3.8 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 7

Characterization complete for class 2 (already known from step maxSlack=2).

Characterization complete for class 3 (already known from step maxSlack=3).

Characterization complete for class 4 (already known from step maxSlack=0).

Characterization complete for class 5 (already known from step maxSlack=0).

Characterization complete for class 7 (already known from step maxSlack=3).

Characterization complete for class 8 (already known from step maxSlack=1).

Characterization complete for class 9 (already known from step maxSlack=2).

Characterization complete for class 13 (already known from step maxSlack=1).

Characterization complete for class 14 (already known from step maxSlack=0).

Characterization complete for class 15 (already known from step maxSlack=0).

Characterization complete for class 16 (already known from step maxSlack=0).

Characterization complete for class 17 (already known from step maxSlack=0).

Characterization complete for class 19 (already known from step maxSlack=1).

Characterization complete for class 20 (already known from step maxSlack=3).

Characterization complete for class 21 (already known from step maxSlack=1).

Characterization complete for class 22 (already known from step maxSlack=0).

Characterization complete for class 23 (already known from step maxSlack=1).

3.9 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 8

Characterization complete for class 2 (already known from step maxSlack=2).

Characterization complete for class 3 (already known from step maxSlack=3).

Characterization complete for class 4 (already known from step maxSlack=0).

Characterization complete for class 5 (already known from step maxSlack=0).

Characterization complete for class 6.

Characterization complete for class 7 (already known from step maxSlack=3).

Characterization complete for class 8 (already known from step maxSlack=1).

Characterization complete for class 9 (already known from step maxSlack=2).

Characterization complete for class 13 (already known from step maxSlack=1).

Characterization complete for class 14 (already known from step maxSlack=0).

Characterization complete for class 15 (already known from step maxSlack=0).

Characterization complete for class 16 (already known from step maxSlack=0).

Characterization complete for class 17 (already known from step maxSlack=0).

Characterization complete for class 19 (already known from step maxSlack=1).

Characterization complete for class 20 (already known from step maxSlack=3).

Characterization complete for class 21 (already known from step maxSlack=1).

Characterization complete for class 22 (already known from step maxSlack=0).

Characterization complete for class 23 (already known from step maxSlack=1).

3.10 spatprog -problem rspd -order sc -minSlack 0 -maxSlac 9

Characterization complete for class 2 (already known from step maxSlack=2).

Characterization complete for class 3 (already known from step maxSlack=3).

Characterization complete for class 4 (already known from step maxSlack=0).

Characterization complete for class 5 (already known from step maxSlack=0).

Characterization complete for class 6 (already known from step maxSlack=8).

Characterization complete for class 7 (already known from step maxSlack=3).

Characterization complete for class 8 (already known from step maxSlack=1).

Characterization complete for class 9 (already known from step maxSlack=2).

Characterization complete for class 13 (already known from step maxSlack=1).

Characterization complete for class 14 (already known from step maxSlack=0).

Characterization complete for class 15 (already known from step maxSlack=0).

Characterization complete for class 16 (already known from step maxSlack=0).

Characterization complete for class 17 (already known from step maxSlack=0).

Characterization complete for class 19 (already known from step maxSlack=1).

Characterization complete for class 20 (already known from step maxSlack=3).

Characterization complete for class 21 (already known from step maxSlack=1).

Characterization complete for class 22 (already known from step maxSlack=0).

Characterization complete for class 23 (already known from step maxSlack=1).

4. Characterization of the classes over the 10 step(s)

Correspondence between class number and class description

Class number Class description
1 sHSP database class 1
2 sHSP database class 2
3 sHSP database class 3
4 sHSP database class 4
5 sHSP database class 5
6 sHSP database class 6
7 sHSP database class 7
8 sHSP database class 8
9 sHSP database class 9
10 sHSP database class 10
11 sHSP database class 11
12 sHSP database class 12
13 sHSP database class 13
14 sHSP database class 14
15 sHSP database class 15
16 sHSP database class 16
17 sHSP database class 17
18 sHSP database class 18
19 sHSP database class 19
20 sHSP database class 20
21 sHSP database class 21
22 sHSP database class 22
23 sHSP database class 23

 

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 247      632 126 40 40 40 20 7 5 3 2 ET SG V.V E.G V.K E..V E..K R..E R..R E.....V V.....P G.....V G.....F A....G......P K......V V......G D......E A.......E D........V E........A V......K E.........D R.........R sat 1
2 ok 107      step 2 41 10 0 LP PG ER VL KF PE PP D.P I.V V.V G.R R.E KF..P K..P ok 2
3 ok 47      step 3 185 177 1 0 GER VL PF GV DW WH ER RV DW.ET L.V D.F G.L E.E G..W A..D P...D P...L ok 3
4 ok 16      step 0 0 RKFRLP YL AR ok 4
5 ok 14      step 0 0 PLW VDW ok 5
6 ok 66      step 8 232 60 38 11 9 2 2 2 0 GVL GL PG KE VK IK S.R L.I E.K K.G N..L L..K G..K K..V K...K..V L...M M....L L.....G R.....L V.....E L........L ok 6
7 ok 80      step 3 25 3 2 0 DV PW MP PG KE ED VK AE PK K.R V.D D.P E..K R...PG F...G ok 7
8 ok 15      step 1 1 0 VPG DW KD VK PK SK DW.E K.Q I.V NV ok 8
9 ok 164      step 2 546 63 0 TR RR R.D P.K A.R R..A..A P.K..R R..K ok 9
10 sat 311      1792 1792 1792 1792 1792 1792 1792 1792 1792 unsat G.L sat 10
11 unsat 314      unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat unsat 11
12 sat 258      1025 1025 1025 1025 1025 606 243 unsat unsat unsat R...R R........P S.........P sat 12
13 ok 120      step 1 111 0 RG FQ QG RG.Q F.G W.G ok 13
14 ok 25      step 0 0 ALPGP ok 14
15 ok 25      step 0 0 FRTEIKI ok 15
16 ok 31      step 0 0 PQEF ok 16
17 ok 75      step 0 0 PWY LG AE ok 17
18 sat 155      79 79 79 79 79 79 79 79 79 79 CN sat 18
19 ok 23      step 1 1 0 AE ET LS FS PE PE CS EG PE.V S.K Q.S ok 19
20 ok 96      step 3 94 43 12 0 LL TG GF AG GG P.G P.S L..L E..L F...G A...L G...L T...P ok 20
21 ok 102      step 1 989 0 EQ V.L E.L C.C ok 21
22 ok 13      step 0 0 DEEL SKP ok 22
23 ok 26      step 1 1 0 MSD KA KE DK K.F ok 23
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:  shspdb.xml 

Elapsed time: 299.5 seconds.

 

 

retour gH    Retour à la page principale de   (gH)