Plant and Animal Genome XXI Conference

January 11 - 16, 2013

UCSC Genome Browser Workshop

The UCSC Genome Browser provides a graphical framework for viewing annotations on many sequenced animal genomes in a uniform interface. Other useful tools are tightly integrated into the system. This workshop will familiarize participants with functionality of the Browser and associated tools. For best effect, participants should bring a fully charged laptop and expect to follow along in real time. For each organism, the Browser shows many datasets, including alignment of all mRNAs for all organisms in GenBank mapped to the coordinate system of each animal. This serves to annotate gene locations by homology even in poorly annotated animals that have limited mRNAs in the GenBank repository. Comparative genomics resources allow easy navigation between animal assemblies and access to syntenic regions in other organisms. The Blat tool is used for locating/aligning user sequences and the Table Browser enables mining of the extensive database (and user-uploaded data as well), including intersections and filters. The Browser provides a framework for showing user data as Custom Tracks co-displayed with resident data tracks, using a choice of 15 data formats, including VCF, BAM and Personal Genome SNP formats. pgSNP is used to show locations where sequence from an individual sample from a High-Throughput Sequencing experiment differs from the reference assembly. The Sessions tool allows a user to save the state of the Browser, including personal data, for easy sharing and future access. The Browser software is free for non-commercial use and may be configured to display annotations on any genome sequence.