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We present here LOCATE, a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set. Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were(More)
PlantsP and PlantsT allow users to quickly gain a global understanding of plant phosphoproteins and plant membrane transporters, respectively, from evolutionary relationships to biochemical function as well as a deep understanding of the molecular biology of individual genes and their products. As one database with two functionally different web interfaces,(More)
MOTIVATION High-density microarray technology permits the quantitative and simultaneous monitoring of thousands of genes. The interpretation challenge is to extract relevant information from this large amount of data. A growing variety of statistical analysis approaches are available to identify clusters of genes that share common expression(More)
LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of mouse and human proteins. Over the past 2 years, the data in LOCATE have grown substantially. The database now contains high-quality localization data for 20% of the mouse proteome and general localization annotation for nearly(More)
Biomedical text mining and other automated techniques are beginning to achieve performance which suggests that they could be applied to aid database curators. However, few studies have evaluated how these systems might work in practice. In this article we focus on the problem of annotating mutations in Protein Data Bank (PDB) entries, and evaluate the(More)
BioLit is a web server which provides metadata describing the semantic content of all open access, peer-reviewed articles which describe research from the major life sciences literature archive, PubMed Central. Specifically, these metadata include database identifiers and ontology terms found within the full text of the article. BioLit delivers these(More)
Innovation in computational biology research is predicated on the availability of published methods and computational resources. These resources facilitate the generation of new hypotheses and observations both on the part of the creators and the scientists who use them. These methods and resources include Web servers, databases, and software, both complex(More)
Visualization of functional and structural features of biological macromolecules is an important aspect of communicating and analyzing biological data, for example the presence of a transmembrane domain in relation to a nucleotide binding site or the organization of transcription factor binding sites in a promoter. However, this is not necessarily a trivial(More)
DNA arrays have become the immediate choice in the analysis of large-scale expression measurements. Understanding the expression pattern of genes provide functional information on newly identified genes by computational approaches. Gene expression pattern is an indicator of the state of the cell, and abnormal cellular states can be inferred by comparing(More)