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Protein Sequence Universe10PSU Goal: Enhance annotation resources withanalytic and visualization (browser) tools.Project sequence data into 3D usingmultidimensional scaling (MDS).MDS interpolation allows expanding the universewithout time consuming all vs all O(N 2 )3D map allows much faster interpolationVisualizing PSUECMLS 2012
Multi-Dimensional Scaling (MDS)11Sammon‘s objective function ijHnijf( ij) d(xi,xis dissimilarity measure between sequences i and jd is Euclidean distance between projections x i and x jDenominator: larger contribution from smallerdissimilaritiesf is monotone transformation of dissimilarity measurechosen “artistically”f( ij)j)2Visualizing PSUECMLS 2012
Page 1 and 2: VISUALIZING THE PROTEINSEQUENCE UNI
Page 3 and 4: Grand Challenge of Functional Genom
Page 5 and 6: COG: Clusters of Orthologous Groups
Page 7 and 8: Clustering 10 million UniRef1007Use
Page 9: Public Resources9 Struggle to cope
Page 13 and 14: MDS Details13 f chosen heuristicall
Page 15 and 16: 3D View of 100K COG Sequences15Visu
Page 17 and 18: Cluster Annotation17COG Annotation
Page 19 and 20: Dendrogram of Cluster Centroids19Vi
Page 21 and 22: Heatmap for Selected Clusters21Visu
Page 23 and 24: Blast 623Visualizing PSUECMLS 2012
Page 25 and 26: 25ClusterDataBlast 6Originalrun has
Page 27 and 28: OctTree for 100Ksample of Fungi27We
Page 29 and 30: Conclusions29Data → Knowledge: pr
Page 31 and 32: References and Resources31COG data
Page 33: 25Thank you for your attentionVisua

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