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© Arne Elofsson

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1. Summary


SubCon is a new ensemble method for improved subcellular localization prediction in Human. SubCons combines up to five predictors methods, SherLoc2, LocTree2, MultiLoc2, CELLO2.5 and YLoc (the latest two if available) using a random forest classifier. LocTree2 requires PSSM. To speed up the creation of PSSM file, we use our tool PRODRES (more info at https://github.com/ElofssonLab/PRODRES). PRODRES is faster in createing PSSM profile and it has the same accuracy as Psi-Blast. It is recomended to read carefully the instruction and install it! However, SubCons runs Psi-Blast as alternative to PRODRES (THIS MAKE SUBCONS MUCH SLOWER)



2. Usage


Input to the server is an amino acid sequence in FASTA format. The user can either submit paste one or more sequences in the text-area provided, or, alternatively, upload a file for batch submission of sequences).

Example input:
>sp|P04201|MAS_HUMAN
MDGSNVTSFVVEEPTNISTGRNASVGNAHRQIPIVHWVIMSISPVGFVENGILLWFLCFR
MRRNPFTVYITHLSIADISLLFCIFILSIDYALDYELSSGHYYTIVTLSVTFLFGYNTGL
YLLTAISVERCLSVLYPIWYRCHRPKYQSALVCALLWALSCLVTTMEYVMCIDREEESHS
RNDCRAVIIFIAILSFLVFTPLMLVSSTILVVKIRKNTWASHSSKLYIVIMVTIIIFLIF
AMPMRLLYLLYYEYWSTFGNLHHISLLFSTINSSANPFIYFFVGSSKKKRFKESLKVVLT
RAFKDEMQPRRQKDNCNTVTVETVV



3. Output


see the example output



4. References


SubCons: [Please cite this paper if you find the method SubCons useful in your research]
SubCons: a new ensemble method for improved human subcellular localization predictions. Salvatore, M., Warholm, P., Shu, N., Basile, W., Elofsson, A. Bioinformatics, 2017 Apr 12. [Epub ahead of print] [PubMed]

SubCons Webserver: [Please cite this paper if you find the SubCons web-server useful in your research]
The SubCons web-server: A user friendly web interface for state-of-the-art subcellular localization prediction. Salvatore, M., Shu, N., Elofsson, A. Protein Sci. 2017 Sep 13. doi: 10.1002/pro.3297 [Epub ahead of print] [PubMed]


5. Contact


Arne Elofsson group

Department for Biochemistry and Biophysics
The Arrhenius Laboratories for Natural Sciences
Stockholm University
SE-106 91 Stockholm, Sweden

Science for Life Laboratory
Box 1031, 17121 Solna, Sweden

E-mail:   arne@bioinfo.se
Phone:   (+46)-8-16 4672
Fax:   (+46)-8-15 3679