can be retrieved via the ‘Get DNA’ utility, the Table Browser (14) or direct download (see below). The Table Browser also serves as a tool for retrieving and exploring Genome Browser data through ﬁltering, intersecting and correlating the underlying database tables. Output from the Table Browser can also be sent to other tools such as Galaxy (15) or GREAT (see ‘New features’ section) for subsequent analysis. The BLAT (16) and in silico PCR tools align sequences to genomes available in the browser. The LiftOver utility, available as both a web interface (at http://genome.ucsc.edu/cgi-bin/hgLiftOver) and a command-line executable program (from http:// hgdownload.cse.ucsc.ed/admin/exe/) translates genomic coordinates between assemblies. The Gene Sorter (17) allows users to explore the relationships between genes by comparing expression proﬁles, protein homology and other useful metrics of similarity. The Proteome Browser displays protein properties and sequence data as tracks and histograms (18). VisiGene (19) is a searchable database of Xenopus and mouse in situ images showing cytology and expression patterns. Users can upload and view their data in the context of the other browser tracks using the custom tracks tool (8). Once uploaded, custom track data can be manipulated using any of the standard Genome Browser functionalities including the Table Browser. Track display conﬁgurations can also be saved and shared using the Sessions tool (8). Finally, Genome Graphs displays hosted tracks and user-generated custom tracks in the context of a genome-wide view. Bulk downloads of sequence and annotation data and Genome Browser source code can be found at http:// hgdownload.cse.ucsc.edu/. The source includes the browser bioinformatic command-line utilities (http:// genomewiki.ucsc.edu/index.php/Kent_source_utilities). Instructions for setting up a mirror are available at http:// genome.ucsc.edu/admin/mirror.html. Assemblies and data of interest can also be mirrored selectively (see http:// genomewiki.ucsc.edu/index.php/Minimal_Browser_ Installation). NEW FEATURES Gene search The gene search box takes a user directly to the UCSC/ Known Genes or RefSeq record associated with a gene of interest, bypassing the default search of the entire database (see Figure 1). After two or more characters are entered, the search box suggests gene names, and upon selection of a particular gene, the gene’s coordinates appear in the position/search bar. In cases where the gene has several isoforms, the gene region is immediately dis- played rather than requiring the user to ﬁrst select a par- ticular isoform, thus eliminating an extra navigation step. Drag-reorder Tracks within the browser image can now be reordered more easily by clicking on the label or vertical bar to the left of the track and dragging it to a new position within the image. If the track is a member of a composite track, hovering over the bar will cause the bars of all related Nucleic Acids Research, 2011, Vol. 39, Database issue D877 subtracks to turn blue, making it easier to distinguish the reordered subtracks that belong to a single composite track. Tracks can be restored to their default order via a button below the track image (see Figure 2). BigBed/BigWig and BAM ﬁle support In late 2009 we introduced two new ﬁle formats for very large data sets, BigBed and BigWig (20), and have continued to add support for the display of these ﬁles as built-in tracks and custom tracks. BigWig and BigBed ﬁles are compressed binary indexed ﬁles containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the Genome Browser. A big advantage of these ﬁle formats is that only the portions of the ﬁles needed to display a particular region are transferred to UCSC, enabling fast remote access to large distributed data sets. We have also introduced support for the Binary Alignment/Map (BAM) ﬁle format in custom tracks and in multi-view composite tracks. BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format (21), a compact and indexable representation of nucleotide sequence alignments. BAM ﬁle format employs an architecture similar to BigWig/BigBed ﬁles and thus segments of the BAM ﬁle are transmitted as needed to display the current browser view, unlike PSL and other human-readable alignments formats. This makes it possible to load very large BAM ﬁles as custom tracks in situations where the ﬁle size would preclude upload in other ﬁle formats. BAM custom tracks enable the display of high-coverage sequencing read align- ments from the 1000 Genomes Project (http://www .1000genomes.org/), other sequencing projects, and the underlying data from which SNPs and CNVs were called. (See the Neandertal Sequence Reads track in Figure 2 for an example of the BAM track display.) Display enhancements We have augmented the Genome Browser’s wiggle and microarray track display functionalities. Log-transformed wiggle data values may now be viewed in the browser, and we have also added a new windowing function for viewing wiggle data at zoomed-out levels. When a zoom-level is too large to show individual data values, the values must be combined to produce a plot point. With the ‘mean+whiskers’ function, it is possible to simultaneously view the mean data value overlaid with measures of its central tendency. The mean appears in a dark shade, 1 standard deviation around the mean in a medium shade, and the maximum/minimum in a light shade. Another new display feature is the transparent, multicol- ored overlay of multiple wiggles for some tracks (for an example, see Raney et al. in this issue). Standard and custom microarray tracks can be viewed in one of ﬁve combinations of red, green, blue, and yellow by selecting a scheme on the track details page (Figure 1) or by specifying an ‘expColor’ value in the custom track’s settings (see http://genomewiki.cse.ucsc.edu/index.php/ Microarray_track#Microarray_Custom_Tracks).