A region-based approach to shape representation and similarity measure is presented. The shape representation is invariant to translation, scale and rotation. The similarity measure conforms to human similarity perception, i.e., perceptually similar shapes have high similarity measure. An experimental shape retrieval system has been developed and its performance has been studied. The shape retrieval performance of the proposed approach is better than that of the more established Fourier descriptor method.

BackgroundSmall RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction.ResultWe have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram.ConclusionsWe have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.miRPlant and its manual are freely available at http://www.australianprostatecentre.org/research/software/mirplant or http://sourceforge.net/projects/mirplant/.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-275) contains supplementary material, which is available to authorized users.

UDDI is a standard for publishing and discovery of web services. UDDI registries provide keyword searches for web services. The search functionality is very simple and fails to account for relationships between web services. In this paper, we propose an algorithm which retrieves closely related web services. The proposed algorithm is based on singular value decomposition (SVD) in linear algebra, which reveals semantic relationships among web services. The preliminary evaluation shows the effectiveness and feasibility of the algorithm.

Supplementary data are available at Bioinformatics online.