DEVELOPMENTAL DYNAMICS 235:747–753, 2006

TECHNIQUES

Piloting the Zebrafish Genome Browser

Anthony DiBiase,1*† Rachel A. Harte,2† Yi Zhou,1 Leonard Zon,1 and W. James Kent2

This correspondence is a primer for the zebrafish research community on zebrafish tracks available in the UCSC Genome Browser at http://genome.ucsc.edu based on Sanger’s Zv4 assembly. A primary capability of this facility is comparative informatics between humans (as well as many other model organisms) and zebrafish. The zebrafish genome sequencing project has played important roles in mutant mapping and cloning, and comparative genomic research projects. This easy-to-use genome browser aims to display and download useful genome sequence information for zebrafish mutant mapping and cloning projects. Its user-friendly interface expedites annotation of the zebrafish genome sequence. Developmental Dynamics 235:747–753, 2006. © 2005 Wiley-Liss, Inc.

Key words: zebrafish; browser; mapping

Accepted 9 November 2005

INTRODUCTION veloped the capability for researchers major re-assembly when compared to to view the zebrafish genome. Zv3) is available today as danRer2.It The Trans-NIH Zebrafish Genome The best zebrafish genome assem- is this assembly that will be the focus of Project Initiative has started to pro- blies available today still exhibit a high this report. Truth be told, the 1.56 giga- vide useful tools for researchers. In- degree of mis-assembly even in Zv5, bases of sequence (about 5.7ϫ coverage) ternational collaboration and fore- which has just been released and is in Zv4 assembly is still preliminary. Zv5 sight (especially the Wellcome Trust downloadable from http://www. has 1.63 gigabases of sequence with a Sanger Institute and UCSC’s Genome sanger.ac.uk/Projects/D_rerio/Zv5_ coverage of 6.5–7ϫ as more reads have Informatics Group) have rapidly de- assembly_information.shtml). Zv4 (a been sequenced (Sanger Institute,

ABBREVIATIONS danRer2 UCSC danio rerio (zebrafish) build 2 BLAST Basic local alignment sequence tool BLAT BLAST-like Alignment Tool chr[1–25, Un, NA, M] Zebrafish chromosome names: chr1-chr25, chrUn, ChrNA, chrM contig A continuous sequence of DNA that has been assembled from overlapping cloned DNA fragments FASTA Text file format commonly used as input to BLAST FPC fingerprinted contig GUI graphical user interface PSL text file format for representing sequence alignments SNPs single nucleotide polymorphisms STS markers Sequence Tagged Site marker represents a single, unique, sequence-defined point in a genome supercontig A supercontig consists of one or more sequence contigs known to occur in a specific order and orientation TIGR The Institute for Genome Research (now part of the Craig Venter Institute) Track mode The UCSC genome browser displays tracks in one of the following modes: Hide: the track is not displayed at all. Dense: the track is displayed with all features collapsed into a single line. Full: the track is displayed with each annotation feature on a separate line. Squish: the track is displayed with each annotation feature shown separately, but at 50% the height of full mode. Pack: the track is displayed with each annotation feature shown separately and labeled, but not necessarily displayed on a separate line Vega Sanger’s Vertebrate Genome Annotation database is a central repository for high quality, frequently updated, manual annotation of vertebrate finished genome sequence WGS whole genome shotgun sequencing method WZ EST clusters Washington University at St. Louis zebrafish EST clusters ZGC NCBI zebrafish genome collection Zv5 Sanger’s Zebrafish assembly version 5.

1Division of Hematology/Oncology, Children’s Hospital, Karp Research Laboratories, Boston, Massachusetts 2Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California Grant sponsor: National Human Genome Research Institute (NHGRI); Grant sponsor: Howard Hughes Medical Institute (HHMI); Grant sponsor: NIH; Grant number: RO1 DK05538. †Anthony DiBiase and Rachel A. Harte contributed equally to this work. *Correspondence to: Division of Hematology/Oncology, Children’s Hospital, Karp Research Laboratories, Boston, MA 02115. E-mail: [email protected] DOI 10.1002/dvdy.20661 Published online 21 December 2005 in Wiley InterScience (www.interscience.wiley.com).

© 2005 Wiley-Liss, Inc. 748 DiBIASE ET AL.

2004). At the top level, the danRer2 tively, this box may be used to search WZ EST Clusters (clustered ESTs assembly is organized as: for accession names, gene names, or from Washington University, St. names of scientists who deposited se- Louis), Non-Zebrafish mRNAs, TIGR quences in GenBank. This is outlined Gene Index. chr1 to chr25: finished clones on the Gateway page. Expression and Regulation: Affy matched to WGS supercontigs. The default track display may be Zebrafish Genechip: alignment of se- chrNA: WGS contigs that could not altered using the track display con- quences used for probe design. be related to any FPC contig. trols in the bottom half of the browser Comparative Genomics: Human, chrUn: WGS supercontigs that page and by clicking on the “configure Mouse, Opossum, Fugu and Tetraodon mapped to FPC contigs, unknown tracks and display” button. Pull-down Chain/Human, Mouse, Opossum, Fugu chromosome. menus set the display mode for each and Tetraodon Net/6- Way Conservation chrM: mitochondrion genome se- track and are explained at the link and Most Conserved (Zebrafish/Tetra- quence was obtained from NCBI. http://genome.ucsc.edu/goldenPath/ odon/Fugu/Human/Mouse/Opossum help/hgTracksHelp.html#TRACK_ multiple alignment and conservation)/ Having put the browser infra- CONT. Human Proteins (tBLASTn of Human structure and development re- All tracks have hide, dense, and full Known Genes). sources in place, our team is ready to modes while some additionally pos- Variation and Repeats: Repeat- greet each new, improved release of sess squish and pack modes. Clicking Masker/Simple Repeats. the zebrafish assembly and quickly on a the track title above the track Links to various tools reside on the blue process it for the research communi- controls or the blue or gray bar per- bar along the top of the browser. BLAT is ty’s use as part of the UCSC Genome pendicular to a track on the track dis- a very useful tool for aligning sequences Browser (Kent et al., 2002). play takes the user to the page de- to the genome. It is a tool similar to This primer is organized to allow re- scribing the track, its creation, data BLAST but allows rapid alignment searchers to rapidly perform informat- sources, and credits. Some tracks, against very large sequences such as ge- ics analyses. We first present the basic such as the ESTs tracks, have filters nomes (Kent et al., 2002). The “Tables” elements of the graphical user interface on this page that allow the user to link leads to the Table Browser where (GUI). Next, is a brief discussion of the select features with certain character- regions of the genome may be selected available genomic tracks (viewable us- istics, e.g., organism, author, tissue of and data may be filtered and downloaded ing the browser GUI and represented as origin, etc. Clicking on a feature from the underlying database tables that colored, collinear blocks with text labels within a track will bring up a details contain the browser data (Karolchik et and strand annotation) and their sa- page with additional feature-specific al., 2004). The “PDF/PS” tool produces a lient characteristics. Next, we present information. This may include links to PDF or PostScript (PS) file of the image of some cookbook recipes for tasks that re- alignments or to additional external the current view in the browser. The searchers routinely perform. We close information depending on the type of “Help” link provides information on get- with a glimpse into the next release of track. Other tracks have the facility to ting started with using the Genome and the browser. obtain the DNA from the region of the the Table Browsers. feature with such options as repeat Downloads of sequence and align- BROWSER GUI AND masking and for acquiring the DNA ment data for the whole genome may with additional upstream and down- be obtained from the “Downloads” link TRACKS stream regions and the sequence may on the blue bar at the left side The zebrafish browser may be ac- be reverse complemented. The DNA or from: http://hgdownload.cse.ucsc.edu/ cessed through the Gateway page for link on the blue bar at the top of the downloads.html the genome browser (http://genome. browser also performs a similar func- Selecting the Zebrafish link takes the ucsc.edu/cgi-bin/hgGateway). Zebra- tion. For the tracks belonging to the user to a list of available downloads. fish should be selected from the pull- Genes and Gene Predictions Group, The Full data set includes the repeat down list of genomes and an assembly there is the ability to select 5Ј UTR, masked (using RepeatMasker and Tan- date may be chosen from the assembly coding region (CDS) or 3Ј UTR exons dem Repeat Finder) genome sequence menu. Currently, the Zv4 (UCSC for genomic DNA. The mRNA se- with repeats either in lowercase or re- name: danRer2) Zebrafish assembly quence and predicted protein se- placed by capital N’s. Different bioinfor- is available (June 2004), although the quence are also available. The ze- matics software may require different next freeze of the assembly (to be brafish (danRer2) release includes formats so we provide these two for- called danRer3) may be accessed in the following tracks: mats. The lowercase masked sequence the near future. A position may be Mapping and Sequencing: Posi- is also available by individual chromo- added to the position box and this may tion, Contigs, Scaffolds, Radiation Hy- some from the “Annotation data by be a chromosome range, e.g., chr1 for brid Map, BAC Ends, Gap, GC Percent, chromosome” link. The zebrafish mR- the whole of chromosome 1 and chr1: Short Match, Restriction Enzymes. NAs, ESTs and RefSeqs, and non-ze- 1,000–4,000 for the region from Genes and Gene Prediction: Ref- brafish mRNAs are available for down- 1–4,000 on chromosome 1 (Fig. 1). Af- Seq Genes, ZGC Genes, Ensembl load from the full data set. The ter submitting this information, the Genes. “Annotation database” link provides the default browser view for the chosen mRNA and EST: Zebrafish mR- data and a means of recreating the ze- position will be displayed. Alterna- NAs and ESTs, spliced ESTs, ZFish brafish database that is behind the ge- PILOTING THE ZEBRAFISH GENOME BROWSER 749 nome browser. BLASTz (Schwartz et you to the tracks page. When you click page opens a window whose title is al., 2003) Fugu, human, and mouse on the colored descriptor text “gmb3” similar to “Alignment of danRer2_ alignments versus zebrafish are also in the left-hand margin, you are taken refGene_NM_213308 and chr1: available together with the correspond- to the page “RefSeq Gene.” From here, 43721385-43722734.” ing chains and nets data. you can download sequence for pre- BLAT is a BLAST-like Alignment The “Comparative Genomics” link dicted protein, mRNA sequence, or Tool, which is fast and suitable for at http://zfrhmaps.tch.harvard.edu/ genomic sequence. aligning sequences to a very large se- ZonRHmapper also displays recipro- Two recipes for downloading multi- quence such as a genome (Kent, 2002). cal pre-BLAST results between hu- ple sequences using genomic descrip- The BLAT link may be found on the man known genes and Fugu tors follow. blue bar of the Index (http:// proteins, and between zebrafish ge- genome.ucsc.edu), Gateway, and Ze- nome sequences and Fugu proteins. Download all BAC End Pairs brafish browser pages. First select the In addition, a BLAST (Altschul et in a genomic region using a list zebrafish genome from the “Genome” al., 1990) search engine is available of constraints. and “Assembly” menu pull-downs on to meet specific needs. the BLAT page. The query type may From the gateway page, click on the be selected as DNA, protein, trans- “Tables” link on the blue bar atop the RECIPES lated RNA, or translated DNA. page (Karolchik et al., 2004). Select “BLAT’s guess” is the default and it is General notes: Tracks are bold, e.g., “Mapping and Sequencing Tracks” good at distinguishing between a DNA Human net. GUI buttons are dou- from the “group” pull-down menu. Se- and protein query. Generally, the hy- ble-quoted, e.g. “submit.” Genome lect “Radiation Hybrid Map” from the perlink output is good if you wish to be builds are bold italics, e.g., danRer. track pull-down menu. Select the “po- able to view the alignment in the “Sample position queries” on the sition” region radio button, and enter browser and also the aligned se- gateway page http://genome.ucsc.edu/ a position in the text box (say: chr19: quences. However, in order to obtain a cgi-bin/hgGateway describes a wide 208146-227384). Type a name for your text summary of the alignment and co- range of descriptors you can search for file in the “output file” text box, then ordinates, a PSL output may be chosen. sequence data. Clicking on the blue or click “Get Output.” For more information see http://genome. gray bar at the side of the track or on the Download all the exon peptide ucsc.edu/goldenPath/help/hgTracksHelp. track name above the track control re- html#BLATAlign. sults in a description of the track being sequences for all zebrafish genes displayed. (known to date). 2. Downloading Sequence: We will download an entire table from Determining Human DNA and Amino Acids the database in this recipe. From the Homologs gateway page, click on the “Tables” Two recipes for downloading single se- Human homolog of zebrafish link on the blue bar atop the page. gene. quences using genomic descriptors fol- Select “Genes and Gene predictions” low. from the “group” pull-down menu. Se- Configure the Human Chain track Using a chromosome name and lect either “RefSeq” or “Ensembl” from visibility to pack, then type the gene genomic index. the track pull-down menu. Select the symbol of interest into the “position,” “genome” region radio button. Type a hit enter on your keyboard. Click on From the gateway page, type your po- name for your file in the “output file” the links from the details page. You sitional info (say, chr22:12879-24844) text box, then click “Get Output.” will be directed to the corresponding into the “position” box, then hit enter. regions of the human genome. A spe- Select the “DNA” link from the tracks cific example for the twhh gene is BLATing Sequence page, which will take you to a page shown in Figure 2a and b. entitled “Get DNA in Window.” Set Click on the “BLAT” link on the blue A user may have a zebrafish gene of the Sequence “Retrieval Region and bar atop the Gateway (or any other) interest for which they want to find the Formatting Options,” then click on the page. human homolog. It is possible to start “Get DNA” button on the lower left. Input sequence text: Cut FASTA either by searching for the zebrafish sequence text of interest from a source gene in the browser by searching using Using a gene name. and paste it into large input text box. the gene name in the “Position” box or From the gateway page, type your Input sequence from file: Type in the user can BLAT a sequence of inter- gene descriptor (say, NB) into the “po- or browse to the FASTA file name con- est as described above. Once the gene is sition” box, then hit enter on your key- taining your sequence. in the browser display, human ho- board. You will then be in a page of Click on “submit.” A “BLAT Search mologs can be found by using the pre- hits based on your input. You must Results” window will appear detailing computed human comparison tracks. select (click on a link) for the hits you alignments. Clicking on a “browser” Human Chain and Human Net are specifically interested in. Choos- link from this page takes you to the tracks are useful for viewing these com- ing “BC059436” from the list of the position in the genome with your cur- parative alignments and using the hits under the heading “Zebrafish rent track display configuration. track controls, these may be switched to Aligned mRNA Search Results” takes Clicking on a “details” link from this “full” visibility. The Human Proteins 750 DiBIASE ET AL.

Fig. 1. Zebrafish Genome Browser Gateway Page and its components.

Fig. 2. a: Zebrafish Genome Browser in the region of the twhh gene. Coloring of alignments for the chain, net, and Human Proteins tracks represents the chromosome to which the region is aligned on the other organism’s genome. The Chromosome Color Key is between the browser display and the track controls. Alignment chr12 ϩ 47769k means this alignment is to the Human chromosome 12 on the ϩ strand starting at around co-ordinate 47769k (exact co-ordinates are on the details page found by following the link from this label). chr 7 ϩ 154749k aligns, in part, to the region of the human sonic hedgehog (shh) gene, chr 2 ϩ 219745k aligns to the human indian hedgehog (ihh) gene, and chr7 ϩ 47769k aligns to the human desert hegdehog (dhh) gene. b: Human Genome Browser in the region of the dhh gene. Alignment chr12 ϩ 47769k from the zebrafish browser aligns to the region of the desert hedgehog homolog (dhh) gene on the human genome browser. PILOTING THE ZEBRAFISH GENOME BROWSER 751 track started with predicted proteins from the Known Genes mRNA from human (hg17 assembly, NCBI Build 34). Then, after identifying the exons by BLAT, the corresponding putative ex- ons were found in the zebrafish genome using tBLASTn and, finally, these alignments were “chained” together to form longer alignments to determine gene structure. The human gene names are used as labels for these alignments in the zebrafish browser. On this page, there is a choice of coloring the align- ments: (1) by score with shades of gray representing percent identity; (2) by chromosome color (the key for this is just below the browser track display) or (3) the alignments may be all displayed in black. The Human Chain and Human Net tracks may be used in a similar way. BLASTz (Schwartz et al., 2003) is used to align two genomes and the chaining program chains together alignments to form gene structure. Fig. 3. Zebrafish Browser showing the Human Chains and the Human Net in the region of the Clicking on these alignments will zebrafish atp2a1, ypel3, mapk3, and zgc:77781 genes that have provisional status as RefSeqs. give information about the co-ordi- nates of the alignment on both ge- nomes. There is also a link to the tions, and which chromosomes or chro- text search may again be used to ini- other organism’s browser to show mosomal regions are derived from each tially identify the region of interest (see the region of alignment. With the other. The chain and net tracks can be Fig. 3). BLASTz alignments are first RefSeq and mRNA tracks visible, it used in determining synteny between chained to produce the gene structure is possible to see if there are known genomes (Kent et al., 2003). BLAT or a and some low scoring chains are re- homologs in this region. Alterna- tively, turning on some of the Gene Prediction or EST tracks would suggest whether there is evidence for genes in this particular region.

Determining Synteny Gene synteny to human and mouse. Configure 6-way Conservation, RefSeq Genes, Human Net, and Mouse Net tracks to “full” mode (and any other species net tracks you are interested in). Type the gene symbol of interest into the “position” box, then type enter on your keyboard (if you don’t have a gene name, you can enter a genomic position chrN: start – end). A new window displays a list of possi- ble zebrafish gene candidates. Click on a desired link in this list. Use the zoom controls near the top of the page to focus. See the details below for con- tent and explanations. Syntenic regions can provide clues to how one genome evolved from another and so one can see the inversions, dele- Fig. 4. Custom annotation tracks available in the danRer2 build. 752 DiBIASE ET AL. moved at this stage. The BLASTz same scaffold so it is likely that they using the info at http://genome. blocks are in the same orientation and are from the same chromosome and ucsc.edu/goldenPath/customTracks/ order in each species in order to be also show conserved synteny. Gaps in custTracks.html. chained. In the production of the net this top level chain are filled in by track (see Human Net track in Fig. other chains at level 2, which may also FUTURE TRACKS 2a), the highest scoring alignment is have gaps filled in by chains in level 3 chosen and this is displayed at level 1 in but there are no chains for level 2 gaps In the future, new tracks of interest to this track. Only orthologous regions are in this case. Annotation of the level the zebrafish research community will shown. 2–6 alignments indicates whether be added to the browser. Here are If the position, chr3:16,170,001- these alignments are syntenic (Syn), some possibilities: 16,270,001, is copied into the position inverted (Inv), or non-syntenic (Non- Mapping and Sequencing: Up- box and the Human, Mouse, and Te- Syn) in relation to the gap in the level date (Zv5 assembly). traodon Net tracks turned to “full” as above. In Figure 3, there are several Genes and Gene Prediction: in Figure 3, it can be seen that there green alignments in level 2, which are Vega, KnownGenes. are alignments in levels 1 and 2 of also aligned to human chromosome Variations and Repeats: STS these net tracks. The top level (1) is 12, and these are non-syntenic since markers, SNPs. the largest, highest scoring chain in they do not align to the same chromo- Vega genes (http://vega.sanger.ac. this region. The boxes represent un- some as the gap above in level 1. uk) is a set of manually curated anno- gapped alignment while the lines rep- tations from The Wellcome Trust Sanger Institute, Cambridge, United resent gaps and arrows show the di- Finding Markers in Gene rection of the alignment on the query Kingdom. Annotations are produced Locus genome (human in this case). Clicking at the clone level by similarity on a line displays details about that Download all RH markers in a searches against DNA and protein da- tabases as well as using ab initio gene gap, while clicking on a box gives de- genomic region using a list of predictions. Genome comparisons be- tails about the alignment with a link constraints. to show the actual alignment or to link tween evolutionarily closely related to the corresponding region in the ge- From the gateway page, click on the species are also used to extend anno- nome browser for the query. The Ref- “Tables” link on the blue bar atop the tations. All of the data are useful in Seq and mRNA tracks show the gene page. Select “Mapping and Sequenc- adding gene structures, polyA fea- structure for the genes in zebrafish in ing Tracks” from the “group” pull- tures, and gene descriptions to the ge- this region: there are four genes with down menu. Select “Radiation Hybrid nome. The Known Genes track will be annotations (atp2a1, ypel3, mapk3, Map” from the track pull-down menu. created for the Zv5 assembly (dan- and zgc:77781). In level 1, the align- Select the “position” region radio but- Rer3) and this will consist of protein- ment is mainly light blue, showing ton, and enter a position in the text coding genes based on the Ensembl that it is aligned to human chromo- box (say: chr19:208146-227384). Type gene set (Curwen et al., 2004). Links some 16. The equivalent regions for a name for your file in the “output file” to other data sources such as in situ the mouse are pink indicating align- text box, then click “Get Output.” hybridization images (at ZFIN, http:// ment to chr7 and for tetraodon the zfin.org), protein structures, will be green shows alignment to chrUn_ran- available through the details pages for Translating Coordinates the genes. dom, which are unmapped scaffolds. Between Assemblies For Human and Mouse Nets, there We welcome and encourage sugges- is an alignment that corresponds to When a new assembly is released, the tions for new and interesting tracks the position of the atp2a1 gene and coordinates for many annotation fea- from our users. There is a genome another that contains the region of the tures may change. A user may wish to browser mailing list (genome@soe. ypel3, zgc:77781, and mapk3 genes. In be able to find features of interest in a ucsc.edu) to which you may subscribe. all cases, these alignments are on the new assembly and to be able to trans- Here, users may make suggestions, par- same chromosome for each species. late the co-ordinates from an older as- ticipate in discussions, or ask questions Since these genes and alignments are sembly to the current one. From the about using various features of the found on the same chromosome within Index, Gateway, or Browser pages, genome browser. Subscription may be each species, they exhibit conserved the “Help” link can be selected. The set up from this site: http://www.cse. synteny. For tetraodon, there is one “Convert” link from the blue bar ucsc.edu/mailman/listinfo/genome. In alignment with the atp2a1 gene re- across the top of the screen explains addition, new features and releases are gion, another with ypel3 and zgc:7778, how to convert data between assem- announced through the genome-an- and a third with the mapk3 gene re- blies. nounce mailing list to which a subscrip- gion. These are all on chrUn_random tion may be set up from this site: http:// www.soe.ucsc.edu/mailman/listinfo/ in tetraodon and if a block in the CUSTOM ANNOTATION aligning region is clicked, the details genome. TRACKS page is displayed and a link can be followed to the corresponding region Figure 4 details the custom annota- ACKNOWLEDGMENTS in the tetraodon browser. This shows tion tracks available in the danRer2 We thank all members of the Boston that these three alignments are on the build. You can add your own tracks Children’s Hospital Zebrafish Genome PILOTING THE ZEBRAFISH GENOME BROWSER 753

Initiative. We also thank all members tional Human Genome Research In- 2004. The UCSC Genome Browser Data- of the Genome Bioinformatics Group stitute (NHGRI) and the Howard base. Nucleic Acids Res 32:D493–D496. at UCSC and also the many collabora- Hughes Medical Institute (HHMI). Kent WJ. 2002. BLAT: The BLAST-like alignment tool. Genome Res 12:656–664. tors who have contributed sequence The Zebrafish Genome Initiative at Kent WJ, Sugnet CW, Furey TS, Roskin and annotation data to our project, as Children’s Hospital Boston is funded KM, Pringle TH, Zahler AM, Haussler D. well as the UCSC Genome Browser by NIH grant RO1 DK05538. 2002. The human genome browser at users for their feedback and support. UCSC. Genome Res 12:996–1006. Many thanks to Donna Karolchik for Kent WJ, Baertsch R, Hinrichs A, Miller browser documentation and to the fol- REFERENCES W, Haussler D, Kent WJ. 2003. Evolu- lowing people from UCSC who created tion’s cauldron: duplication, deletion, and rearrangement in the mouse and hu- tracks on the zebrafish danRer2 Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment man genomes. Proc Natl Acad Sci USA browser: Andy Pohl (Restriction En- search tool. J Mol Biol 215:403–410. 100:11484–11489. zymes), Mark Diekhans (ZGC genes), Curwen V, Eyras E, Andrews TD, Clarke Sanger Institute. 2004. Zebrafish Sequenc- Brian Raney (Human Proteins), and L, Mongin E, Searle SMJ, Clamp M. ing Group data. ftp://ftp.sanger.ac.uk./ Hiram Clawson (Opossum Chains and 2004. The Ensembl automatic gene an- pub/sequences/zebrafish [last accessed Net). Many thanks for QA of the dan- notation system. Genome Res 14:942– December 2005]. Rer2 browser go to Jennifer Jackson, 950. Schwartz S, Kent WJ, Smit A, Zhang Z, Karolchik D, Baertsch R, Diekhans M, Baertsch R, Hardison RC, Haussler D, Robert Kuhn, Ali Sultan-Qurraie, and Furey TS, Hinrichs A, Lu YT, Roskin Miller W. Human-mouse alignments Galt Barber. The UCSC Genome KM, Schwartz M, Sugnet CW, Thomas with BLASTZ. 2003. Genome Res 13:103– Browser project is funded by the Na- DJ, Weber RJ, Haussler D, Kent WJ. 107.