SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q7RX84 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MASADMSPSRSHPHDATRSPSPRTQSPSPRDEDGSRSPGERTPSPPSRDP    50
  51  SPYRSPGERTPSPSPRRDRSLSPRDQPHSHPRSRSPTPRSQSPSRRSVRS   100
 101  PSPRQGSPARRVDRSSSPRARSPPPRRHSRSPPLRGQPPPPRHRDAGGDY   150
 151  RPVRKERTPTPPPVAVKTEEEKLADARAEYQKLLNLRSQGVYLPPHRLRA   200
 201  LQAAITDKKTREYQRMAWEALKKSVNGLVNKVNTANIKFVVPELFGENLI   250
 251  RGRGLFCQSLLKAQHASLPFTPIYACLAAICNTKLPQVGELLVKRLVLRF   300
 301  RKAFKRNDKAVCLSSTMFIAHLVNNQVVHEMIAAQILLLLLAKPTDDSVE   350
 351  IAVGLMREVGLFLEEMSPAIAHAVFDQFRNILHEADIDRRTQYMIEVLFQ   400
 401  VRKDKYKDNPVIKEELDLVEEEDQITHRIGLDDEIDPQDGLNVFKMDPNW   450
 451  EENEEEYKKLKAEILGEASDDDEDDDDDDESESGSESEDEEQKALEIKDQ   500
 501  SNADLVNLRRTIYLSIQSSADPEEAAHKLMKLRLPAGQEAELVSMIVESC   550
 551  AQEKVYLKFMGLLGERFARLNRMWMDLFEESFAKYYSTIHRYETNKLRNI   600
 601  ARFFGHLLATDAIGWHVFSVIHLNEEETTSASRIFIKILFEDLQENIGSA   650
 651  KLKARMSEETLQPSLQGIFPHDEPRNIRFSINYFTSIKMGYLTDEMRTFL   700
 701  ANMPKPALPAPPADSDSESVSSYSSYSSYSSRSRSRSLTPRKDTRGRSLS   750
 751  RTPPRRGRGRSYSRTPSRSRSRSRSYSRSVSKSVSRSPPRRRAVESRSPS   800
 801  PPPRGRGRSYDRYSRSPSRSRSRTRSPAAAPPIRRGRSGTRSRSRSYSRS   850
 851  PSPPPARGYPTRGRAPVSNNDRAAAASGKRRREGSYSASRSPHPPPQQRL   900
 901  RRGSYSRSRSRSPIPIRGNGPAGRDTGRAGPAPARGGRRNRSYSRSRTRS   950
 951  PPPLADAATGSRRVVSRSPSPVVGNNKRRRSYSSSRSRSRSSSRSRYRSR  1000
1001  SPVAKRGRVD                                          1010

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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