Nucleic Acids Research, 2009, Vol. 37, Database issue D759 Figure 2. Screen image of Genome Browser for hg18 human assembly, chromosome 1, showing several new features. From top to bottom: Scale bar; UCSC Genes track; Non-human RefSeq Genes; TransMap RefSeq Genes, showing improved mapping of bases at 30-end of a mouse RefSeq (red) that did not map in Non-Human RefSeq track; Conservation track; SNP 129 track. Entire image has been reversed from default conﬁguration using Reverse button (cursor arrow at bottom) to show Transmap annotations in 50-to-30 direction. Figure 3. Gene Sorter output showing new columns for the TP53 gene (top row) and all genes meeting the criterion, Protein Homology–BLASTP. Columns shown, left to right: BLASTP E-value, Genome Position, Exon Count, Intron Size (set to maximum size) and Coding SNPs (truncated). eliminates the need to scroll up or down the page to submit a change. A number of enhancements have been made ‘under the hood’ to improve the performance of the Genome Browser. To reduce the number of track controls beneath the browser image and to speed the refresh of the page, certain groups of related tracks have been combined into super-tracks that share conﬁguration options. For example, the individual tracks within the TransMap track on vertebrate assemblies are controlled together. Track controls for super-tracks are distinguished by an ellipsis (. . . ) in the label name. The details pages of multiple alignment tracks now allow users to obtain DNA sequences from low-coverage assemblies for which no genome browser is provided. The in silico PCR function now creates a track on the Genome Browser image, allowing the user to visualize the relationship between an ampliﬁed fragment and other annotations, most usefully exons and introns. When the primers used to generate the amplicon do not match the reference assembly, the browser highlights the diﬀerences with red coloration. Custom tracks enhancements The custom track feature of the UCSC Genome Browser allows users to view their own data in the context of all the resident data on the browser. We have enhanced this fea- ture in several ways. For example, the ‘next item’ feature, previously available only for selected UCSC-hosted tracks, is now available for a broader set of tracks