Visualizing the genome: techniques for presenting human genome data and annotations.
BACKGROUND
In order to take full advantage of the newly available public human genome sequence data and associated annotations, biologists require visualization tools ("genome browsers") that can accommodate the high frequency of alternative splicing in human genes and other complexities.


RESULTS
In this article, we describe visualization techniques for presenting human genomic sequence data and annotations in an interactive, graphical format. These techniques include: one-dimensional, semantic zooming to show sequence data alongside gene structures; color-coding exons to indicate frame of translation; adjustable, moveable tiers to permit easier inspection of a genomic scene; and display of protein annotations alongside gene structures to show how alternative splicing impacts protein structure and function. These techniques are illustrated using examples from two genome browser applications: the Neomorphic GeneViewer annotation tool and ProtAnnot, a prototype viewer which shows protein annotations in the context of genomic sequence.


CONCLUSIONS
By presenting techniques for visualizing genomic data, we hope to provide interested software developers with a guide to what features are most likely to meet the needs of biologists as they seek to make sense of the rapidly expanding body of public genomic data and annotations.
Loraine
Ann E
AE
Bioinformatics Department, Affymetrix, Inc, 6550 Vallejo Street, Ste 100, Emeryville, CA 94608, USA. ann_loraine@affymetrix.com
Helt
Gregg A
GA
D017398:Alternative Splicing / Q000235:genetics; D001483:Base Sequence / Q000235:genetics / Q000502:physiology; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data*; D003196:Computer Graphics / Q000639:trends*; D003628:Database Management Systems / Q000639:trends*; D030541:Databases, Genetic / Q000145:classification / Q000639:trends; D005091:Exons / Q000235:genetics / Q000502:physiology; D005796:Genes / Q000235:genetics / Q000502:physiology; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D007438:Introns / Q000235:genetics / Q000502:physiology; D020033:Protein Isoforms / Q000145:classification / Q000235:genetics / Q000502:physiology; D011506:Proteins / Q000145:classification / Q000235:genetics / Q000502:physiology; D017422:Sequence Analysis, DNA
D020033:Protein Isoforms; D011506:Proteins