Genome Environment Browser (GEB) – tutorial (December 2006)

Genome Environment Browser (GEB) user guide GEB is a Java application developed to provide a dynamic graphical interface to visualise the distribution of genome features and chromosome-wide experimental data in high resolution. (I) Genome Features Annotated in GEB The demonstration (“demo”) version of GEB provides annotation for human (NCBI Build 36, Ensembl database version 50.36i) and mouse (NCBI Build 36, Ensembl database version 46.36g) genomes. GEB can display data from any genomes available at Ensembl if custom GEB databases have been built (please refer to the GEB installation guide). In each demo genome, the following standard features were annotated: 1. Genes: Exon-intron location of protein-coding genes was obtained from Ensembl. Both Ensembl known and novel (predicted) genes were included. In addition, where a gene produces more than one transcript (e.g. through alternative splicing or alternative promoter usage), information for individual transcript is available. 2. Non-coding genes: Non-coding genes annotated by Ensembl. They include: pseudogenes (processed and unprocessed), tRNA (nuclear transfer RNA, or pseudogene), mt-tRNA (mitochondrially-derived tRNA pseudogenes located in nuclear genome), rRNA(ribosomal RNA or pseudogene), scRNA(small cytoplasmic RNAor pseudogene), snRNA (small nuclear RNA or pseudogene), snoRNA (small nucleolar RNA or pseudogene) and miRNA (microRNA precursors or pseudogene), misc_RNA (miscellaneous ...