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 . ____________________________^_________________

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