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home maria private gallery work nt pt st women others ico vasko assen nushi museum		Antigenic antigenic/emboss Kolaskar and Tongaonkar Jameson and Wolf Clustered systers Proclust protonet Clustr Various Pathways: pathway-guide in contrast to nucleotide composition in genomes, amino-acid comp. in proteomes is similar across kingdoms. aa-distribution as in Rost "Did evolution leap.." 2002. Motifs Motifscanner 3D analysis PDBSUM: Enter PDB code (4 characters) Meta-predict protein Fischers Structure Alignment compilation Hhpred PipeAlign PONDR DisEMBL Globplot2 DISOPRED2 PDISORDER PredictProtein Gene ontology Ontoexpress (Web-based, Java GUI, all GO-cat, 4 stat tests, needs login, very slow): automatically translates lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. GoMiner (stand-alone windows, organism specific IDs, total genome as reference set for Pvalue) Genemerge (-) (web and stand-alone, abstracts to lowest level, one cat at a time, KEGG for fly and yeast, needs refernce upload, hypergeometric - uses FBgn, with GeneNameconverter) Funcassociate (web, CG, abstracts to lowest level) GOstat user can choose between 2 stat tests, total genome as ref for Pvalue, understands all from fb GOToolBox (web-based, organism specific ids, choice of 3 tests, total genome as ref for Pvalue) FBgn, CG FatiGO (web-based, organism specific ids, one GO cat at a time, total genome as ref for Pvalue) FBgn, CG - percentage eGOn needs login, allows user to collapse and expand nodes GOTM needs login, allows the user to collapse and expand nodes, understands CG numbers, but is not the optimal visualizatioor p Expression E-northern Alignment SPEM (2d based), Muscle, probcons, T-coffee treeview, phylodendron Fibrillar stuff coil matcher Interaction databases EMBL-Cellzome-interactions intact Evaluate-confirm structure visualization: pymol vmd Evaluate structure model using Prosa2003, Verify3D, ProQ and/or MaxSub surface projection of conservation: consurf, rate4site DALI- checks if fold correct, similarity by pseudo-energy Z-score biotech procheck- checks stereochemistry Errat Verify3D anolea- check spatial features compiled from high resolution protein structures hubmed Endeavour for the computational prioritisation of `test genes', based on a set of `training genes'.

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