SchistoDB: an updated genome resource for the three key schistosomes of humans - PubMed (original) (raw)

. 2013 Jan;41(Database issue):D728-31.

doi: 10.1093/nar/gks1087. Epub 2012 Nov 17.

Eric R G R Aguiar, Fudong Yu, Huayong Xu, Yixue Li, Neil D Young, Robin B Gasser, Anna V Protasio, Matthew Berriman, David S Roos, Jessica C Kissinger, Guilherme Oliveira

Affiliations

SchistoDB: an updated genome resource for the three key schistosomes of humans

Adhemar Zerlotini et al. Nucleic Acids Res. 2013 Jan.

Abstract

The new release of SchistoDB (http://SchistoDB.net) provides a rich resource of genomic data for key blood flukes (genus Schistosoma) which cause disease in hundreds of millions of people worldwide. SchistoDB integrates whole-genome sequence and annotation of three species of the genus and provides enhanced bioinformatics analyses and data-mining tools. A simple, yet comprehensive web interface provided through the Strategies Web Development Kit is available for the mining and visualization of the data. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, gene ontology terms, sequence motifs, protein characteristics and phylogenetic relationships. Search strategies can be saved within a user's profile for future retrieval and may also be shared with other researchers using a unique web address.

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Figures

Figure 1.

Figure 1.

Screen shot of the SchistoDB homepage. (A) The banner section present on all SchistoDB webpages provides links to registration, login, and contact us forms, ID and text searches, information and help, and all available searches and tools. (B) The side panel on the homepage provides expandable tabs that reveal links to a data summary table, community news items, links to community resources, web tutorials and additional information and help links. (C) The central portion of the home page includes all available searches and tools—gene-specific searches, searches against other data types such as genomic sequence, open reading frames and ESTs and tools, such as BLAST, sequence retrieval and the genome browser.

Figure 2.

Figure 2.

Screen shot of a search strategy with the first step being the results of running the search shown in Figure 1C (inset). The ‘Add Step’ button reveals a popup with all available searches in SchistoDB. The results of any search are displayed in a dynamic table that allows removing, adding and moving columns, downloading results and adding results to the basket.

References

    1. Rollinson DA. Wake up call for urinary schistosomiasis: reconciling research effort with public health importance. Parasitology. 2009;136:1593–1610. - PubMed
    1. Young ND, Jex AR, Li B, Liu S, Yang L, Xiong Z, Li Y, Cantacessi C, Hall RS, Xu X, et al. Whole-genome sequence of Schistosoma haematobium . Nat. Genet. 2012;44:221–225. - PubMed
    1. Protasio AV, Tsai IJ, Babbage A, Nichol S, Hunt M, Aslett MA, De Silva N, Velarde GS, Anderson TJC, Clark RC, et al. A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni . PLoS Negl. Trop. Dis. 2012;6:e1455. - PMC - PubMed
    1. Zerlotini A, Heiges M, Wang H, Moraes RLV, Dominitini AJ, Ruiz JC, Kissinger JC, Oliveira G. SchistoDB: a Schistosoma mansoni genome resource. Nucleic Acids Res. 2009;37:D579–D582. - PMC - PubMed
    1. Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, et al. The genome of the blood fluke Schistosoma mansoni . Nature. 2009;460:352–358. - PMC - PubMed

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