NEMBASE: a resource for parasitic nematode ESTs - PubMed (original) (raw)

NEMBASE: a resource for parasitic nematode ESTs

John Parkinson et al. Nucleic Acids Res. 2004.

Abstract

NEMBASE (available at http://www.nematodes.org) is a publicly available online database providing access to the sequence and associated meta-data currently being generated as part of the Edinburgh-Wellcome Trust Sanger Institute parasitic nematode EST project. NEMBASE currently holds approximately 100 000 sequences from 10 different species of nematode. To facilitate ease of use, sequences have been processed to generate a non-redundant set of gene objects ('partial genome') for each species. Users may query the database on the basis of BLAST annotation, sequence similarity or expression profiles. NEMBASE also features an interactive Java-based tool (SimiTri) which allows the simultaneous display and analysis of the relative similarity relationships of groups of sequences to three different databases. NEMBASE is currently being expanded to include sequence data from other nematode species. Other developments include access to accurate peptide predictions, improved functional annotation and incorporation of automated processes allowing rapid analysis of nematode-specific gene families.

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Figure 1

Figure 1

Screenshots from a typical search strategy on NEMBASE. [1] Annotation search page: on this page users may either retrieve a cluster by entering its ID or the ID of one of its constituent sequences (a) or select a species and enter some text to search for keywords in the BLAST annotation associated with clusters from that species (b). Output may be viewed in terms of relative abundance, BLAST score or using the SimiTri Java tool (c). [2] SimiTri output page: selecting the SimiTri output option creates the embedded Java applet (d); individual clusters are represented by coloured tiles on the graphic. The relative position of the tiles indicates the clusters’ relative similarity to the three selected data sets. Clusters with similarity to only one or no data set are listed below the applet (e). Clicking on a tile whilst holding the control key held down, or selecting a cluster from the list below the applet launches the detailed cluster page [3]. This provides information on the number and source of the constituent sequences, summaries of BLAST annotation and further links to e.g. raw trace chromatograms [4] associated with the sequences.

References

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