Table 1. Summary of new UCSC Genes track UCSC Genes Coding Noncoding Total Genes 53 036 13 767 66 803 Clusters 20 409 6161 26 570 Previous 20 433 5871 26 304 Change 24 +290 +266 The latest UCSC Genes annotation uses the CCDS pro- tein to determine the proper alignment where the CCDS and RefSeq are not in perfect agreement. At the time when we made this decision, it was our belief that the beneﬁts of an international consensus outweighed minor diﬀerences in gene models resulting from arbitrary choices of align- ment in tandemly duplicated regions and minor diﬀer- ences in opinion on the true 50-end of a transcript. This has led us to choose CCDS over RefSeq for start codons or splice sites of 353 genes, for example, the splice junc- tions between exons 4 and 5 in the gene IFI35 (at hg18 chr17:38,418,889-38,419,044, http://genome.ucsc.edu/cgi- bin/hgTracks?db=hg18&position=chr17:38418889-3841 9044&knownGene=pack&refGene=pack). The new UCSC gene set contains 66 803 genes (including isoforms) of which 13 767 are nonprotein- coding genes (Table 1). The genes are found in 26 570 clusters. This update includes links in the Genome Browser to and from external databases for the orthologous genes in several model organisms: the Mouse Genome Database, MGD (30), the Rat Genome Database, RGD (27), Zebraﬁsh Information Network, ZFIN (31), WormBase (C. elegans) (32), FlyBase (Drosophila) (33) and Saccha- romyces Genome Database (34). We plan to continue providing regular updates of the UCSC Genes track for the latest human and mouse assemblies. To view the UCSC Genes annotation for a speciﬁc gene using the Genome Browser, type a search term into the Position box on the Genome Browser webpage. It is pos- sible to search on a wide variety of gene identiﬁers, such as HGNC names (35) or UniProt ID as well as keywords from the GenBank or UniProt descriptive text. The latter approach will also ﬁnd genes whose products are associated with each other, provided the association is annotated in the RefSeq text. The details pages for the UCSC Genes track contain links to local resources such as the Gene Sorter, Proteome Browser and the VisiGene in situ hybridization image archive as well as links to a wide variety of external data- bases. New linkouts this year include Human Cortex Gene Expression data from the Allen Brain Institute, Human Genome Epidemiology (HuGE) data (36) and the Com- parative Toxicogenomics Database (CTD) (37). Variation The hg18 human assembly oﬀers a number of human var- iation annotations, several of which have been updated in the past year. Of particular note, we have added SNP data from dbSNP release 129 (38) to supplement the existing dbSNP data from the 128 and 126 releases on the human hg18 assembly. Nucleic Acids Research, 2009, Vol. 37, Database issue D757 The Genome Browser details pages for the SNP 129 annotation track have been expanded to capture much of the data from the dbSNP database, including the type of SNP (coding, noncoding, synonymous, etc.). We now also display the alignment to the reference assembly of the region surrounding the SNP. Additionally, for compara- tive purposes, the orthologous alleles from several primate species (chimp, orangutan and rhesus) are given. Figure 1 shows part of the SNP 129 details page for SNP rs1128456. We have also updated the mm9 SNP annotation to dbSNP version 128 and have released dbSNP 127 on the bosTau3 cow assembly. A new annotation track in the Comparative Genomes group on the hg18 assembly, Cons Indels MmCf, uses evolutionary conservation among human, mouse and dog to identify small indels in the human reference assem- bly. Other new variation data tracks on hg18 (all in the Variation and Repeats track group) include DGV Structural variants, Segmental Dups, Exapted Repeats and Interrupted Repeats. UCSC has removed data from the Wellcome Trust Case Control Consortium study and the NIMH study of bipo- lar disorder in response to the policy decision by NIH that these data could potentially be used to identify individuals under certain circumstances, in possible violation of the terms of consent for the studies. We will continue working with other groups in the international research community to determine how best to protect the conﬁdentiality of participants of genome-wide association studies (GWAS), while making these data accessible for scientiﬁc research. Depending on the outcome of these discussions, we plan to provide more GWAS data in the Genome Browser in the future, as well as new graphical tools for viewing and analyzing clinical trial data. Transmap A group of new data tracks, known collectively as TransMap, has been added to all vertebrate genome assemblies in the Genes and Gene Prediction group. These tracks map genes and related annotations in one species to another, using synteny-ﬁltered pairwise genome alignments (chains and nets) to determine the most likely orthologs. Individual tracks within the TransMap supertrack include mappings based on, respec- tively, mRNA, RefSeq or UCSC Genes evidence (39). For the mRNA TransMap track on the human assembly, for example, more than 400 000 mRNAs from 23 vertebrate species were aligned at high stringency to the native assem- bly using BLAT. The alignments were then mapped to the human assembly using the chain and net alignments pro- duced using Blastz (40), which has higher sensitivity than BLAT for diverged organisms. Compared with translated BLAT (Non-Human RefSeq Genes, Figure 2), TransMap ﬁnds fewer paralogs and aligns more UTR bases (Figure 2). For closely related low-coverage assemblies, a reciprocal–best relationship is used in the chains and nets to improve the synteny prediction. As with all GBD annotations, the details of the dataset construction may be