TY - Generic T1 - Epiviz: interactive visual analytics for functional genomics data. Y1 - 2014 A1 - Chelaru, Florin A1 - Smith, Llewellyn A1 - Goldstein, Naomi A1 - Bravo, Héctor Corrada KW - algorithms KW - Chromosome mapping KW - Data Mining KW - database management systems KW - Databases, Genetic KW - Genomics KW - Internet KW - software KW - User-Computer Interface AB -

Visualization is an integral aspect of genomics data analysis. Algorithmic-statistical analysis and interactive visualization are most effective when used iteratively. Epiviz (http://epiviz.cbcb.umd.edu/), a web-based genome browser, and the Epivizr Bioconductor package allow interactive, extensible and reproducible visualization within a state-of-the-art data-analysis platform.

JA - Nat Methods VL - 11 CP - 9 M3 - 10.1038/nmeth.3038 ER - TY - JOUR T1 - Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics JF - Bioinformatics (Oxford, England)Bioinformatics (Oxford, England) Y1 - 2005 A1 - Haft, Daniel H. A1 - J. Selengut A1 - Brinkac, Lauren M. A1 - Zafar, Nikhat A1 - White, Owen KW - Chromosome mapping KW - database management systems KW - Databases, Genetic KW - documentation KW - Gene Expression Profiling KW - Gene Expression Regulation KW - Genomics KW - Information Storage and Retrieval KW - Microbiological Techniques KW - natural language processing KW - Prokaryotic Cells KW - Proteome KW - signal transduction KW - software KW - User-Computer Interface KW - Vocabulary, Controlled AB - MOTIVATION: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics. RESULTS: We have created a Genome Properties system to present key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties. AVAILABILITY: Genome Properties can be found at http://www.tigr.org/Genome_Properties SUPPLEMENTARY INFORMATION: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl. VL - 21 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15347579?dopt=Abstract ER -