The choice of localisation algorithms may be determined by the proteins you wish
to predict. Do you have a sequence or IDs. What species? Have a look at SUBA3: http://suba.plantenergy.uwa.edu.au for 22 programs we use for Arabidopsis proteins. There is also a consensus predictor that uses all of them and experimental data. The listed predictors are linked so you can find more information on individual predictors. In the attached publication, there is a figure that shows which predictor is working for which compartment, so if you are looking for a particular compartment. I personally think YLoc, MultiLoc are quite good when predicting across all compartments and surpass WolF PSORT in terms of MCC for some compartments (more about this is in the pipeline for publication if you are interested). Most of these tools may be transferrable to your species. I hope that helps.
kind regards
Conny
Article SUBA3: A database for integrating experimentation and predic...
It is difficult to say which program is best but you may find lot of software packages in OSDDlinux, try http://osddlinux.osdd.net/
Dear Cornelia Thanks a lot for beneficial information. I have sequences from nono LC/MS for sunflower proteins. so thanks for attached publication
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