Visualization techniques for genomic data.
In order to take full advantage of the newly available public human genome sequence data and associated annotations, biologists require visualization tools that can accommodate the high frequency of alternative splicing in human genes and other complexities. In this article, we describe techniques for presenting human genomic sequence data and annotations in an interactive, graphical format, with the aim of providing developers with a guide to what features are most likely to meet biologists' needs. These techniques include: one-dimensional semantic zooming to show sequence data alongside gene structures; moveable, adjustable tiers; visual encoding of translation frame to show how alternative transcript structure affects encoded proteins; and display of protein domains in the context of genomic sequence to show how alternative splicing impacts protein structure and function.
Loraine
Ann E
AE
Affymetrix, Inc., Emeryville, CA 94608, USA. ann_loraine@affymetrix.com
Helt
Gregg A
GA
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D003628:Database Management Systems; D016678:Genome; D016247:Information Storage and Retrieval / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface