We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome in the collection, symmetrically. A new, intelligently scaled alignment display makes it simple to view all changes between the genomes at all levels of resolution, from substitutions to complex structural rearrangements, including duplications.
@article{arxiv.1311.1241,
title = {Comparative Assembly Hubs: Web Accessible Browsers for Comparative Genomics},
author = {Ngan Nguyen and Glenn Hickey and Brian J. Raney and Joel Armstrong and Hiram Clawson and Ann Zweig and Jim Kent and David Haussler and Benedict Paten},
journal= {arXiv preprint arXiv:1311.1241},
year = {2013}
}