This directory contains alignments of the following assemblies: - target/reference: Zebrafish (danRer3, May 2005, Sanger Centre, Danio rerio Sequencing Project Zv5) - query: Human (hg18, Mar. 2006, NCBI Build 36) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - danRer3.hg18.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - danRer3.hg18.net.gz: "net" file that describes rearrangements between the species and the best Human match to any part of the Zebrafish genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - axtNet/*.danRer3.hg18.net.axt.gz: chained and netted alignments, i.e. the best chains in the Zebrafish genome, with gaps in the best chains filled in by next-best chains where possible. The axt format is described in http://genome.ucsc.edu/goldenPath/help/axt.html . The chainSwap program was used to translate hg18-referenced chained blastz alignments to danRer3 into danRer3-referenced chains aligned to hg18. See the download directory goldenPath/hg18/vsDanRer3/README.txt for more information about the hg18-referenced blastz and chaining process. Lineage-specific repeats were not used for alignments involving zebrafish chrUn and chrNA. Instead, the M parameter was set to 50 in order to use the dynamic masking functionality of Blastz. Chained alignments were processed into nets by the chainNet, netSyntenic, and netClass programs. Best-chain alignments in axt format were extracted by the netToAxt program. All programs run after blastz were written by Jim Kent at UCSC. ---------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory goldenPath/danRer3/vsHg18/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all files in the current directory) All files in this directory are freely available for public use. -------------------------------------------------------------------- References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte, F., Yap, V.B., and Miller, W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002). Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489 (2003). Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-mouse alignments with BLASTZ. Genome Res. 13(1), 103-7 (2003).