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

NucPred

Fetching Q9HDY9 from www.uniprot.org...

The NucPred score for your sequence is 0.19 (see score help below)

   1  MSIALAFFILVLLGFSWASPSALDDTFNVSRSVGLISSSNLESCQSSPLE    50
  51  VGNIYNSTSASEILSTLDAKYITIIGVIGSSNSSIQDLIDSVGNSNNAAS   100
 101  SNPTSTVTEYVDRVQTVTEYVTLSCGQAFTSTVDISSSTSSSVINSPTGT   150
 151  AVSSQISTLSMSPSSTPVFSPSASVSSKVASSVSYVSSEPSDSSSSTNTV   200
 201  ILTTSVNSPAVSSSETLTSVSITSTESAYTSSSVDIAASTTASSTLPVST   250
 251  SEATVSFSTDIPATPSTLSSPASSSSSYLVETSSTLTDSVFTTVTATSDS   300
 301  SVITYTLINSVTSSSETTNLPSSSSSLVTIGESSFPSSLLSLLTQSFSTV   350
 351  RSTSSSSTDQLTSASPISSSVISPSVSSPTSSILTNSGSIKSGDHQIVTT   400
 401  SFVQTTTHGSQVETLTYVTTLTETILTTTYDSHTFLTTITPSPSNSISYT   450
 451  NNTFIPSSSIKSSIVYSVTPTSAENYTSSEAFSTSSSLVVIPPVNSSLVT   500
 501  SSTSFTKFSSLSSSQLSTENFTSASSSLSLTNAKSSLSTPSTTIPTSNSS   550
 551  VSLQTSSSLIISSPIISSSLTATSTSTPALTHSITPSNTSYTSSLIPSSS   600
 601  TDYSSSLITVCSNVTSEISSTSLASLISTLTSQQISSNKSSEFVGQTTTE   650
 651  YTTSGSVGFTTTLATQSGSVPGTVLVDVPTPSWITETVTSGSVGFTTTIA   700
 701  TPIGTTAGTVLVDIPTPSWVTETVTSGSIGFTTTIATPIGSTAGTVLVDV   750
 751  PTPSWVTETVTSGSVGFTTTIATPIGSTAGTVLVDIPTPSWVTETVTSGS   800
 801  VGFTTTIATPVGTTAGTVLVDIPTPSWVTETVTSGSVGFTTTIATPVGTT   850
 851  AGTVVVDVPTPSWVTETVTSGSVGFTTTIATPIGSTAGTVLVDIPTPSWV   900
 901  TETVTSGSVGFTTTIATPVGTTAGTVLVDIPTPSWVTETVTSGSVGFTTT   950
 951  IATPIGTTAGTVLVDIPTPSWVTETVTSGSVGFTTTIATPVGTTAGTVLV  1000
1001  DIPTPSWVTETVTSGSVGFTTTIATPIGTTAGTVLVDIPQQHATTTTTTT  1050
1051  FDGFSGYTSSYTGSITETIVIGTPHHSVVDVS                    1082

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.)

Go back to the NucPred Home Page.