D756 Nucleic Acids Research, 2009, Vol. 37, Database issue for the scientiﬁc community. All data are freely available via the Genome Browser and Table Browser interfaces, and may be downloaded in bulk at http://hgdown- load.cse.ucsc.edu. The source code and binaries are free for noncommercial use. In addition to the Genome Browser graphical interface, the GBD provides other tools for eﬃcient data mining. The Table Browser (13) continues to be one of the most widely used features of the GBD toolset and is increas- ingly used to export data to the Galaxy (14) tools at Penn State for further processing. The Gene Sorter (15), the Proteome Browser (16), VisiGene (3), Genome Graphs (4) and BLAT (17) have been previously described. UCSC is the Data Coordination Center for the Encyclopedia of DNA Elements (ENCODE) project (18), which uses the GBD and Genome Browser for data storage and graphical access to the data. This project uses a variety of techniques to generate genome-wide anno- tations, including DNase hypersensitivity sites, mRNA expression, histone modiﬁcation, transcription factor binding sites and gene annotations (Gencode). Data deposited for the ENCODE pilot project (now completed) are presented in the Genome Browser as separate track groups on the human hg18 assembly. Initial ENCODE production-phase data will become available in the coming year. The evolving set of tools associated with the GBD has ever-increasing capability and conﬁgurability. Users can ﬁnd assistance in using the database and tools via a large number of online help pages (http://genome.ucsc. edu/goldenPath/help), FAQs (http://genome.ucsc.edu/ FAQ) and links to tutorials produced by Open Helix (http://openhelix.com). We also provide staﬀ resources to address questions from users through our mailing list (genome@soe.ucsc.edu). NEW DATA New assemblies Since the last GBD update paper was written in September 2007 (4), we have added 13 new genome assemblies to the database, including the initial assemblies for nine new organisms (orangutan, marmoset, guinea pig, zebra ﬁnch, lamprey, lancelet, and three Caenorhabditis species: brenneri, remanei and japonica) and updated assemblies for the cow, zebraﬁsh, sea urchin and C. elegans. We pro- vide a basic set of annotations for each new assembly, as well as alignments of GenBank data and pairwise align- ments (chain and net tracks) (19) of the assembly to selected other organisms. Seven of the new assemblies have multiple-alignment annotations, including a compar- ison of six worm species on the latest C. elegans (ce6) browser. New annotations In addition to new assembly releases, more than 200 anno- tations have been added to existing genome assemblies in the past year. These annotations represent a wide variety of data types, including new microarray data for several organisms and a collection of variation data in the human assemblies (see below). This section summarizes a repre- sentative sample of the new annotation data. Further details on the construction of any annotation are easily obtained by clicking on an item in the corresponding track in the Genome Browser. A new annotation on the hg18 human assembly, Pos Sel Genes in the Genes and Gene Prediction track group, shows genes under positive selection in one or more of six mammals (20). The track displays the results of a genome-wide scan for positively selected genes based on multiple alignments of the human, chimp, macaque, mouse, rat and dog genome assemblies. Orthologous genes were examined for evidence of positive selection using a series of nine likelihood ratio tests (LRTs) based on Yang and Nielsen’s (21) branch-site framework. New data from the Open Regulatory Annotation (ORegAnno) project show gene regulation annotations for four model organisms (human, mouse, Drosophila melanogaster, and yeast) (22). An ORegAnno record des- cribes an experimentally proven and published regula- tory region (promoter, enhancer, etc.), transcription factor binding site, or regulatory polymorphism. Each ORegAnno annotation has links to the ORegAnno database. The human assembly now contains annotation data (the HGSV Discordant track) from Kidd et al. (23) that maps clones from eight individuals from the HapMap Project (24) to the reference assembly. This annotation shows regions where the known size of the clone does not match the size of the reference, representing a putative large indel, and provides a valuable source of information and cloned DNA for mapping human genetic variation. A 30-vertebrate alignment Conservation track is now available on the mm9 mouse assembly. This track, which displays the results of a multiz alignment and phastCons computation (25), is useful for viewing the evo- lutionary relatedness of sequences across a wide range of animals. We have also added a dataset to the mm9 assem- bly showing microRNAs from miRBase at the Wellcome Trust Sanger Institute (26). On the rat rn4 assembly we now provide quantitative trait locus (QTL) data from the RGD (27). These data deﬁne more than 1000 loci in the rat genome that aﬀect a phenotypic trait in a continuously distributed fashion, such as blood pressure and glucose level. A new track of more than 7500 gene insertions in D. melanogaster (GDP Insertions) is displayed on the dm3 genome assembly. These annotations allow identiﬁ- cation of genes for which P-element and Minos insertion strains are available from the Gene Disruption Project (28), with a direct link to the stock center in Bloomington for detailed information and ordering. New UCSC Genes In September 2008, we released a new version of the UCSC Genes dataset for the hg18 human assembly. The UCSC Genes annotation includes multiple isoforms of known protein-coding and noncoding genes based on a variety of criteria, including evidence from RefSeq, UniProt (29), GenBank and comparative genomics.