Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

Output format



DESCRIPTION

For each input sequence the following is shown (see the example below):
  • Header line, quoting the name and length of the sequence.

  • Sequence, in one-letter code, as it was interpreted by the server.

  • Annotation overview, showing the predictions residue by residue, as follows:

    . (dot) neutral place-holder
    s predicted to be within a signal peptide
    P predicted to be followed by a propeptide cleavage site

  • Prediction score table, quoting the position, context and score for each arginine (R) and lysine (K) residue in the sequence.

    If the score is >0.5 the residue is predicted to be followed by a propeptide cleavage site; the higher the score the more confident the prediction.

  • Graph, in GIF, illustrating the predictions.

    For each arginine (R) and lysine (K) the prediction score is plotted against the position in the sequence. If a signal peptide cleavage site has been predicted it is also shown in the graph.

The example below shows the output for glial cell line-derived neurotrophic factor precursor (ATF-1), taken from the Swiss-Prot entry GDNF_HUMAN. The signal peptide prediction is consistent with the database annotation. Two propeptide cleavage sites are predicted; one of them (pos. 77-78) is annotated in the database. The other prediction (pos. 168-169) is false.

EXAMPLE OUTPUT


         ##### ProP v.1.0b ProPeptide Cleavage Site Prediction #####


         ##### Furin-type cleavage site prediction (Arginine/Lysine residues) #####


  211 GDNF_HUMAN  
MKLWDVVAVCLVLLHTASAFPLPAGKRPPEAPAEDRSLGRRRAPFALSSDSNMPEDYPDQFDDVMDFIQATIKRLKRSPD      80
KQMAVLPRRERNRQAAAANPENSRGKGRRGQRGKNRGCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCDAAETTYDKIL     160
KNLSRNRRLVSDKVGQACCRPIAFDDDLSFLDDNLVYHILRKHSAKRCGCI                                  240
sssssssssssssssssss.........................................................P...      80
................................................................................     160
.......P...........................................                                  240
 
Signal peptide cleavage site predicted:	between pos. 19 and 20: ASA-FP
 
Propeptide cleavage sites predicted:	Arg(R)/Lys(K): 2




Name           Pos    Context     Score  Pred
____________________________v_________________
GDNF_HUMAN       2    -----MK|LW  0.069    .
GDNF_HUMAN      26    FPLPAGK|RP  0.054    .
GDNF_HUMAN      27    PLPAGKR|PP  0.120    .
GDNF_HUMAN      36    EAPAEDR|SL  0.134    .
GDNF_HUMAN      40    EDRSLGR|RR  0.074    .
GDNF_HUMAN      41    DRSLGRR|RA  0.163    .
GDNF_HUMAN      42    RSLGRRR|AP  0.124    .
GDNF_HUMAN      73    FIQATIK|RL  0.059    .
GDNF_HUMAN      74    IQATIKR|LK  0.140    .
GDNF_HUMAN      76    ATIKRLK|RS  0.062    .
GDNF_HUMAN      77    TIKRLKR|SP  0.802 *ProP*
GDNF_HUMAN      81    LKRSPDK|QM  0.062    .
GDNF_HUMAN      88    QMAVLPR|RE  0.090    .
GDNF_HUMAN      89    MAVLPRR|ER  0.108    .
GDNF_HUMAN      91    VLPRRER|NR  0.146    .
GDNF_HUMAN      93    PRRERNR|QA  0.152    .
GDNF_HUMAN     104    ANPENSR|GK  0.088    .
GDNF_HUMAN     106    PENSRGK|GR  0.071    .
GDNF_HUMAN     108    NSRGKGR|RG  0.099    .
GDNF_HUMAN     109    SRGKGRR|GQ  0.254    .
GDNF_HUMAN     112    KGRRGQR|GK  0.251    .
GDNF_HUMAN     114    RRGQRGK|NR  0.091    .
GDNF_HUMAN     116    GQRGKNR|GC  0.095    .
GDNF_HUMAN     137    GLGYETK|EE  0.058    .
GDNF_HUMAN     143    KEELIFR|YC  0.112    .
GDNF_HUMAN     158    AETTYDK|IL  0.054    .
GDNF_HUMAN     161    TYDKILK|NL  0.067    .
GDNF_HUMAN     165    ILKNLSR|NR  0.072    .
GDNF_HUMAN     167    KNLSRNR|RL  0.070    .
GDNF_HUMAN     168    NLSRNRR|LV  0.767 *ProP*
GDNF_HUMAN     173    RRLVSDK|VG  0.064    .
GDNF_HUMAN     180    VGQACCR|PI  0.080    .
GDNF_HUMAN     201    LVYHILR|KH  0.093    .
GDNF_HUMAN     202    VYHILRK|HS  0.074    .
GDNF_HUMAN     206    LRKHSAK|RC  0.095    .
GDNF_HUMAN     207    RKHSAKR|CG  0.222    .
____________________________^_________________









GETTING HELP

Scientific problems:        Technical problems: