Motivation: PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003. However, the recall needs to be improved and no accurate SCL predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program.Results: We developed PSORTb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies. It features an improved standalone program, with a new batch results delivery system complementing its web interface. We evaluated the most accurate SCL predictors using 5-fold cross validation plus we performed an independent proteomics analysis, showing that PSORTb 3.0 is the most accurate but can benefit from being complemented by Proteome Analyst predictions.Availability: http://www.psort.org/psortb (download open source software or use the web interface).Contact: psort-mail@sfu.caSupplementary Information: Supplementary data are availableat Bioinformatics online.

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Abstract. Both, the number and the size of spatial databases, such as geographic or medical databases, are rapidly growing because of the large amount of data obtained from satellite images, computer tomography or other scientific equipment. Knowledge discovery in databases (KDD) is the process of discovering valid, novel and potentially useful patterns from large databases. Typical tasks for knowledge discovery in spatial databases include clustering, characterization and trend detection. The major difference between knowledge discovery in relational databases and in spatial databases is that attributes of the neighbors of some object of interest may have an influence on the object itself. Therefore, spatial knowledge discovery algorithms heavily depend on the efficient processing of neighborhood relations since the neighbors of many objects have to be investigated in a single run of a typical algorithm. Thus, providing general concepts for neighborhood relations as well as an efficient implementation of these concepts will allow a tight integeration of spatial knowledge discovery algorithms with a spatial database management system. This will speed-up both, the development and the execution of spatial KDD algorithms. For this purpose, we define a small set of database primitives, and we demonstrate that typical spatial KDD algorithms are well supported by the proposed database primitives. By implementing the database primitives on top of a commercial database management system, we show the effectiveness and efficiency of our approach, experimentally as well as analytically. The paper concludes by outlining some interesting issues for future research in the emerging field of knowledge discovery in spatial databases.

Clustering is an important task in mining evolving data streams. Beside the limited memory and one-pass constraints, the nature of evolving data streams implies the following requirements for stream clustering: no assumption on the number of clusters, discovery of clusters with arbitrary shape and ability to handle outliers. While a lot of clustering algorithms for data streams have been proposed, they offer no solution to the combination of these requirements. In this paper, we present DenStream, a new approach for discovering clusters in an evolving data stream. The "dense" micro-cluster (named core-micro-cluster) is introduced to summarize the clusters with arbitrary shape, while the potential core-micro-cluster and outlier micro-cluster structures are proposed to maintain and distinguish the potential clusters and outliers. A novel pruning strategy is designed based on these concepts, which guarantees the precision of the weights of the micro-clusters with limited memory. Our performance study over a number of real and synthetic data sets demonstrates the effectiveness and efficiency of our method.