PMC:540049 / 10010-12149
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/540049","sourcedb":"PMC","sourceid":"540049","source_url":"http://www.ncbi.nlm.nih.gov/pmc/540049","text":"Generic Genome Browser (GBrowse)\nGBrowse (19) is used to visualize genetic and genomic data (Figure 3). Genomic data are extracted from the Ensembl and UCSC genome databases. The Ensembl database is downloaded after each Ensembl release, and the Ensembl API is used to extract the genome features of interest. These are converted into genome feature format (GFF) and loaded into the GBrowse database. From UCSC, certain data types, notably the UCSC mRNA and EST homologies are downloaded, converted into GFF and loaded into the GBrowse database. Currently 32 data tracks are available. Efforts are underway to integrate statistical tools such as selection of tag SNPs (20) and display of D′/R2 plots for an interval of interest.\nAn alternative approach to integrating the Ensembl and UCSC data would be to use distributed annotation server (DAS) (21). However the current specification of DAS only allows a limited glyph set, and does not, for instance, allow graphs to be represented.\nWe make extensive use of the plugin capability provided by GBrowse. A plugin is used to visualize the UCSC dataset of regulatory potential scores (22). This is a very large dataset, which we prefer not to store in our main GBrowse database. Instead, it is imported into a separate database and uses a plugin to connect GBrowse to the data. Similar plugins are used to visualize Fugu net scores and repeat density plots. We expect to add more plugins as we integrate additional data tracks that do not fit the built-in GBrowse model.\nAnother plugin facilitates genome annotation. The plugin uses BLAT (23) to align an mRNA sequence to the genome and convert the result into a GFF file. The user can then upload the file and view the annotation in GBrowse. To add the annotation to the permanent database, the user can email the GFF file to T1DBase, the file is then manually verified and loaded into the database.\nWe also use plugins to allow users to export selected data tracks to a file.\nThe T1DBase GBrowse provides the T1D research community with a rich genomic data environment by integrating the UCSC and Ensembl genomes and user contributed data.","divisions":[{"label":"Title","span":{"begin":0,"end":32}}],"tracks":[{"project":"2_test","denotations":[{"id":"15608258-11586306-76758817","span":{"begin":669,"end":671},"obj":"11586306"},{"id":"15608258-11667947-76758818","span":{"begin":847,"end":849},"obj":"11667947"},{"id":"15608258-15060013-76758819","span":{"begin":1133,"end":1135},"obj":"15060013"},{"id":"15608258-11932250-76758820","span":{"begin":1587,"end":1589},"obj":"11932250"}],"attributes":[{"subj":"15608258-11586306-76758817","pred":"source","obj":"2_test"},{"subj":"15608258-11667947-76758818","pred":"source","obj":"2_test"},{"subj":"15608258-15060013-76758819","pred":"source","obj":"2_test"},{"subj":"15608258-11932250-76758820","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec93b7","default":true}]}]}}