UCSC Genome Browser website surely is one of the must-know sites for both experimental and computational biologists. As their name suggested, it is pretty nice for visualizing and analyzing genomics data without getting bogged down in bioinformatics details. You can even do quite powerful data-mining on your favorite organisms or genes by just a few clicks. A good tutorial for UCSC Genome Browser and also another powerful genome browser called Ensembl can be found here. With the nice, intuitively designed web interface in the front, what happens behind scenes is many programs or utilities being organized together and doing their jobs as integrated pipelines. These utilities (called Kent Source Utilities since they were originally written by Dr. Jim Kent) can be of great help to our own data analysis if we can have a copy of them installed on our local machine. On the UCSC Genome Browser website, they provided access to some of those most commonly used tools for stand alone use. However, this is only a subset of all their tools. If we need to use other tools, we have no choice but to build a copy of our own from their source code. This is what we gonna do in this blog. Continue reading →